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MmPFS (prenylated FMN synthase from Methanosarcina mazei) in complexed with FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Bis-Tris, pH6.5, 2.0M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.34 47.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 306.829 α = 90 b = 134.577 β = 109.211 c = 101.648 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 6M 2023-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.83 48.543 98.6 0.067 1 31.5 19.3 336899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 0.724
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.83 48.543 332990 16360 97.323 0.195 0.1943 0.2027 0.2157 0.2239 RANDOM 39.217
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.686 r_dihedral_angle_3_deg 14.102 r_lrange_it 9.801 r_lrange_other 9.801 r_scangle_other 7.499 r_scangle_it 7.495 r_dihedral_angle_2_deg 7.044 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.218 r_mcangle_other 5.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.686 r_dihedral_angle_3_deg 14.102 r_lrange_it 9.801 r_lrange_other 9.801 r_scangle_other 7.499 r_scangle_it 7.495 r_dihedral_angle_2_deg 7.044 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.218 r_mcangle_other 5.218 r_scbond_it 4.985 r_scbond_other 4.967 r_mcbond_it 3.844 r_mcbond_other 3.844 r_angle_refined_deg 1.46 r_angle_other_deg 0.537 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.199 r_nbd_other 0.199 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_21 0.067 r_ncsr_local_group_38 0.066 r_ncsr_local_group_41 0.066 r_ncsr_local_group_49 0.065 r_ncsr_local_group_55 0.065 r_ncsr_local_group_86 0.065 r_ncsr_local_group_99 0.065 r_ncsr_local_group_80 0.064 r_ncsr_local_group_47 0.063 r_ncsr_local_group_50 0.063 r_ncsr_local_group_63 0.062 r_ncsr_local_group_77 0.062 r_ncsr_local_group_105 0.062 r_ncsr_local_group_18 0.061 r_ncsr_local_group_27 0.061 r_ncsr_local_group_110 0.061 r_ncsr_local_group_151 0.061 r_ncsr_local_group_19 0.06 r_ncsr_local_group_28 0.06 r_ncsr_local_group_35 0.06 r_ncsr_local_group_36 0.06 r_ncsr_local_group_137 0.06 r_ncsr_local_group_31 0.059 r_ncsr_local_group_52 0.059 r_ncsr_local_group_84 0.059 r_ncsr_local_group_129 0.059 r_ncsr_local_group_34 0.058 r_ncsr_local_group_44 0.058 r_ncsr_local_group_59 0.057 r_ncsr_local_group_62 0.057 r_ncsr_local_group_66 0.057 r_ncsr_local_group_70 0.057 r_ncsr_local_group_61 0.056 r_ncsr_local_group_72 0.056 r_ncsr_local_group_102 0.056 r_ncsr_local_group_116 0.056 r_ncsr_local_group_130 0.056 r_ncsr_local_group_142 0.056 r_ncsr_local_group_143 0.056 r_ncsr_local_group_1 0.055 r_ncsr_local_group_24 0.055 r_ncsr_local_group_53 0.055 r_ncsr_local_group_58 0.055 r_ncsr_local_group_78 0.055 r_ncsr_local_group_83 0.055 r_ncsr_local_group_87 0.055 r_ncsr_local_group_7 0.054 r_ncsr_local_group_16 0.054 r_ncsr_local_group_22 0.054 r_ncsr_local_group_73 0.054 r_ncsr_local_group_113 0.054 r_ncsr_local_group_139 0.054 r_ncsr_local_group_147 0.054 r_ncsr_local_group_69 0.053 r_ncsr_local_group_106 0.053 r_ncsr_local_group_134 0.053 r_ncsr_local_group_13 0.052 r_ncsr_local_group_25 0.052 r_ncsr_local_group_46 0.052 r_ncsr_local_group_48 0.052 r_ncsr_local_group_67 0.052 r_ncsr_local_group_103 0.052 r_ncsr_local_group_108 0.052 r_ncsr_local_group_126 0.052 r_ncsr_local_group_127 0.052 r_ncsr_local_group_144 0.052 r_ncsr_local_group_149 0.052 r_ncsr_local_group_43 0.051 r_ncsr_local_group_56 0.051 r_ncsr_local_group_64 0.051 r_ncsr_local_group_82 0.051 r_ncsr_local_group_97 0.051 r_ncsr_local_group_124 0.051 r_ncsr_local_group_145 0.051 r_ncsr_local_group_10 0.05 r_ncsr_local_group_30 0.05 r_ncsr_local_group_118 0.05 r_ncsr_local_group_136 0.05 r_ncsr_local_group_153 0.05 r_ncsr_local_group_5 0.049 r_ncsr_local_group_42 0.049 r_ncsr_local_group_94 0.049 r_ncsr_local_group_98 0.049 r_ncsr_local_group_152 0.049 r_ncsr_local_group_4 0.048 r_ncsr_local_group_33 0.048 r_ncsr_local_group_85 0.048 r_ncsr_local_group_121 0.048 r_ncsr_local_group_132 0.048 r_ncsr_local_group_133 0.048 r_ncsr_local_group_37 0.047 r_ncsr_local_group_60 0.047 r_ncsr_local_group_100 0.047 r_ncsr_local_group_119 0.047 r_ncsr_local_group_138 0.047 r_ncsr_local_group_2 0.046 r_ncsr_local_group_45 0.046 r_ncsr_local_group_65 0.046 r_ncsr_local_group_79 0.046 r_ncsr_local_group_81 0.046 r_ncsr_local_group_9 0.045 r_ncsr_local_group_39 0.045 r_ncsr_local_group_91 0.045 r_ncsr_local_group_117 0.045 r_ncsr_local_group_146 0.045 r_symmetry_xyhbond_nbd_other 0.044 r_ncsr_local_group_3 0.044 r_ncsr_local_group_40 0.044 r_ncsr_local_group_76 0.044 r_ncsr_local_group_88 0.044 r_ncsr_local_group_140 0.044 r_ncsr_local_group_17 0.043 r_ncsr_local_group_68 0.043 r_ncsr_local_group_114 0.043 r_ncsr_local_group_125 0.043 r_ncsr_local_group_8 0.042 r_ncsr_local_group_51 0.042 r_ncsr_local_group_75 0.042 r_ncsr_local_group_92 0.042 r_ncsr_local_group_112 0.042 r_ncsr_local_group_15 0.041 r_ncsr_local_group_74 0.041 r_ncsr_local_group_89 0.041 r_ncsr_local_group_135 0.041 r_ncsr_local_group_148 0.041 r_ncsr_local_group_11 0.04 r_ncsr_local_group_29 0.04 r_ncsr_local_group_32 0.04 r_ncsr_local_group_93 0.04 r_ncsr_local_group_95 0.04 r_ncsr_local_group_111 0.04 r_ncsr_local_group_115 0.04 r_ncsr_local_group_12 0.039 r_ncsr_local_group_20 0.039 r_ncsr_local_group_107 0.039 r_ncsr_local_group_23 0.038 r_ncsr_local_group_26 0.038 r_ncsr_local_group_141 0.038 r_ncsr_local_group_57 0.037 r_ncsr_local_group_101 0.037 r_ncsr_local_group_109 0.037 r_ncsr_local_group_150 0.037 r_ncsr_local_group_54 0.036 r_ncsr_local_group_71 0.036 r_ncsr_local_group_96 0.036 r_ncsr_local_group_123 0.036 r_ncsr_local_group_6 0.035 r_ncsr_local_group_14 0.034 r_ncsr_local_group_122 0.034 r_ncsr_local_group_131 0.034 r_ncsr_local_group_120 0.033 r_ncsr_local_group_128 0.031 r_ncsr_local_group_104 0.025 r_ncsr_local_group_90 0.023 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25288 Nucleic Acid Atoms Solvent Atoms 1432 Heterogen Atoms 678
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing