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Prenylated FMN synthase from Methanosarcina mazei (MmPFS) in complex with prFMN in the radical form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Tris, pH8.5, 2.0M ammonium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 306.848 α = 90 b = 134.876 β = 109.234 c = 101.88 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 1.72 49.4 98.9 0.051 1 36.3 19 408593
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 1.72 1.75 0.727
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 FOURIER SYNTHESIS THROUGHOUT 1.72 19.968 401732 20100 97.117 0.186 0.1851 0.1937 0.2047 0.2119 RANDOM 35.766
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.537 r_dihedral_angle_3_deg 13.539 r_lrange_other 8.869 r_lrange_it 8.864 r_dihedral_angle_2_deg 7.242 r_scangle_other 6.77 r_scangle_it 6.763 r_dihedral_angle_1_deg 5.983 r_scbond_it 4.563 r_scbond_other 4.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.537 r_dihedral_angle_3_deg 13.539 r_lrange_other 8.869 r_lrange_it 8.864 r_dihedral_angle_2_deg 7.242 r_scangle_other 6.77 r_scangle_it 6.763 r_dihedral_angle_1_deg 5.983 r_scbond_it 4.563 r_scbond_other 4.552 r_mcangle_it 4.368 r_mcangle_other 4.368 r_mcbond_it 3.413 r_mcbond_other 3.413 r_angle_refined_deg 1.703 r_angle_other_deg 1.034 r_nbd_refined 0.218 r_nbd_other 0.205 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.142 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.113 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_86 0.069 r_ncsr_local_group_47 0.068 r_ncsr_local_group_61 0.068 r_ncsr_local_group_127 0.067 r_ncsr_local_group_63 0.066 r_ncsr_local_group_21 0.065 r_ncsr_local_group_49 0.064 r_ncsr_local_group_80 0.064 r_ncsr_local_group_137 0.063 r_ncsr_local_group_50 0.062 r_ncsr_local_group_41 0.061 r_ncsr_local_group_56 0.061 r_ncsr_local_group_77 0.061 r_ncsr_local_group_82 0.061 r_ncsr_local_group_110 0.061 r_gen_planes_refined 0.06 r_ncsr_local_group_149 0.06 r_ncsr_local_group_28 0.059 r_ncsr_local_group_70 0.059 r_ncsr_local_group_83 0.059 r_ncsr_local_group_35 0.058 r_ncsr_local_group_69 0.058 r_ncsr_local_group_103 0.058 r_ncsr_local_group_142 0.058 r_ncsr_local_group_129 0.057 r_gen_planes_other 0.056 r_ncsr_local_group_19 0.056 r_ncsr_local_group_55 0.056 r_ncsr_local_group_64 0.056 r_ncsr_local_group_91 0.056 r_ncsr_local_group_102 0.056 r_ncsr_local_group_130 0.056 r_ncsr_local_group_132 0.056 r_ncsr_local_group_133 0.056 r_ncsr_local_group_139 0.056 r_ncsr_local_group_18 0.055 r_ncsr_local_group_27 0.055 r_ncsr_local_group_36 0.055 r_ncsr_local_group_38 0.055 r_ncsr_local_group_44 0.055 r_ncsr_local_group_105 0.055 r_ncsr_local_group_116 0.055 r_ncsr_local_group_144 0.055 r_ncsr_local_group_22 0.054 r_ncsr_local_group_42 0.054 r_ncsr_local_group_67 0.054 r_ncsr_local_group_108 0.054 r_ncsr_local_group_126 0.054 r_ncsr_local_group_147 0.054 r_ncsr_local_group_151 0.054 r_ncsr_local_group_31 0.053 r_ncsr_local_group_99 0.053 r_ncsr_local_group_112 0.053 r_ncsr_local_group_113 0.053 r_ncsr_local_group_118 0.053 r_ncsr_local_group_24 0.052 r_ncsr_local_group_25 0.052 r_ncsr_local_group_34 0.052 r_ncsr_local_group_52 0.052 r_ncsr_local_group_97 0.052 r_ncsr_local_group_134 0.052 r_ncsr_local_group_153 0.052 r_ncsr_local_group_4 0.051 r_ncsr_local_group_10 0.051 r_ncsr_local_group_16 0.051 r_ncsr_local_group_58 0.051 r_ncsr_local_group_59 0.051 r_ncsr_local_group_73 0.051 r_ncsr_local_group_88 0.051 r_ncsr_local_group_1 0.05 r_ncsr_local_group_7 0.05 r_ncsr_local_group_13 0.05 r_ncsr_local_group_30 0.05 r_ncsr_local_group_33 0.05 r_ncsr_local_group_66 0.05 r_ncsr_local_group_72 0.05 r_ncsr_local_group_106 0.05 r_ncsr_local_group_124 0.05 r_ncsr_local_group_140 0.05 r_ncsr_local_group_43 0.049 r_ncsr_local_group_76 0.049 r_ncsr_local_group_79 0.049 r_ncsr_local_group_143 0.049 r_ncsr_local_group_5 0.048 r_ncsr_local_group_62 0.048 r_ncsr_local_group_81 0.048 r_ncsr_local_group_46 0.047 r_ncsr_local_group_53 0.047 r_ncsr_local_group_75 0.047 r_ncsr_local_group_89 0.047 r_ncsr_local_group_100 0.047 r_ncsr_local_group_145 0.047 r_ncsr_local_group_2 0.046 r_ncsr_local_group_40 0.046 r_ncsr_local_group_84 0.046 r_ncsr_local_group_85 0.046 r_ncsr_local_group_94 0.046 r_ncsr_local_group_95 0.046 r_ncsr_local_group_119 0.046 r_ncsr_local_group_121 0.046 r_ncsr_local_group_74 0.045 r_ncsr_local_group_87 0.045 r_ncsr_local_group_93 0.045 r_ncsr_local_group_98 0.045 r_ncsr_local_group_141 0.045 r_ncsr_local_group_11 0.044 r_ncsr_local_group_12 0.044 r_ncsr_local_group_37 0.044 r_ncsr_local_group_57 0.044 r_ncsr_local_group_92 0.044 r_ncsr_local_group_136 0.043 r_ncsr_local_group_148 0.043 r_ncsr_local_group_152 0.043 r_ncsr_local_group_60 0.042 r_ncsr_local_group_122 0.042 r_ncsr_local_group_146 0.042 r_ncsr_local_group_3 0.041 r_ncsr_local_group_8 0.041 r_ncsr_local_group_125 0.041 r_ncsr_local_group_51 0.04 r_ncsr_local_group_78 0.04 r_ncsr_local_group_109 0.04 r_ncsr_local_group_17 0.039 r_ncsr_local_group_115 0.039 r_ncsr_local_group_120 0.039 r_ncsr_local_group_131 0.039 r_ncsr_local_group_14 0.038 r_ncsr_local_group_68 0.038 r_ncsr_local_group_107 0.038 r_ncsr_local_group_6 0.037 r_ncsr_local_group_111 0.037 r_ncsr_local_group_15 0.036 r_ncsr_local_group_45 0.036 r_ncsr_local_group_71 0.036 r_ncsr_local_group_48 0.035 r_ncsr_local_group_54 0.035 r_ncsr_local_group_65 0.035 r_ncsr_local_group_135 0.035 r_ncsr_local_group_29 0.034 r_ncsr_local_group_128 0.034 r_ncsr_local_group_123 0.033 r_ncsr_local_group_138 0.033 r_ncsr_local_group_32 0.031 r_ncsr_local_group_9 0.03 r_ncsr_local_group_26 0.03 r_ncsr_local_group_39 0.03 r_ncsr_local_group_96 0.03 r_ncsr_local_group_101 0.03 r_ncsr_local_group_23 0.028 r_ncsr_local_group_20 0.027 r_ncsr_local_group_90 0.027 r_ncsr_local_group_104 0.026 r_ncsr_local_group_117 0.025 r_ncsr_local_group_114 0.022 r_ncsr_local_group_150 0.019 r_bond_refined_d 0.009 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25236 Nucleic Acid Atoms Solvent Atoms 1545 Heterogen Atoms 768
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing