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F420-dependent glucose-6-phosphate dehydrogenase with glucose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UNK D_1292141271
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NH4F, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.754 α = 90 b = 372.948 β = 90 c = 104.177 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M mirror Si111 2021-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.39 50 99.2 0.154 14.6 11.8 303455 45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.46 95.3 1.082 2.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.393 49.988 303374 15389 99.212 0.174 0.1732 0.1716 0.1909 0.1891 46.268
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] 1.694 0.868 -2.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.245 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_2_deg 8.811 r_dihedral_angle_1_deg 6.608 r_lrange_it 6.49 r_lrange_other 6.489 r_scangle_it 4.672 r_scangle_other 4.672 r_mcangle_it 2.997 r_mcangle_other 2.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.245 r_dihedral_angle_3_deg 14.562 r_dihedral_angle_2_deg 8.811 r_dihedral_angle_1_deg 6.608 r_lrange_it 6.49 r_lrange_other 6.489 r_scangle_it 4.672 r_scangle_other 4.672 r_mcangle_it 2.997 r_mcangle_other 2.997 r_scbond_it 2.959 r_scbond_other 2.959 r_mcbond_it 1.957 r_mcbond_other 1.957 r_angle_refined_deg 1.535 r_angle_other_deg 0.54 r_symmetry_nbd_refined 0.292 r_nbd_other 0.288 r_nbd_refined 0.209 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.07 r_ncsr_local_group_102 0.057 r_ncsr_local_group_105 0.057 r_ncsr_local_group_23 0.054 r_ncsr_local_group_92 0.054 r_ncsr_local_group_108 0.054 r_ncsr_local_group_6 0.053 r_ncsr_local_group_95 0.053 r_ncsr_local_group_51 0.052 r_ncsr_local_group_133 0.052 r_ncsr_local_group_100 0.051 r_ncsr_local_group_107 0.051 r_ncsr_local_group_140 0.051 r_ncsr_local_group_7 0.05 r_ncsr_local_group_22 0.05 r_ncsr_local_group_45 0.05 r_ncsr_local_group_65 0.05 r_ncsr_local_group_98 0.05 r_ncsr_local_group_101 0.05 r_ncsr_local_group_106 0.05 r_ncsr_local_group_120 0.05 r_ncsr_local_group_122 0.05 r_ncsr_local_group_148 0.05 r_ncsr_local_group_27 0.049 r_ncsr_local_group_30 0.049 r_ncsr_local_group_42 0.049 r_ncsr_local_group_52 0.049 r_ncsr_local_group_56 0.049 r_ncsr_local_group_59 0.049 r_ncsr_local_group_90 0.049 r_ncsr_local_group_119 0.049 r_ncsr_local_group_149 0.049 r_ncsr_local_group_14 0.048 r_ncsr_local_group_64 0.048 r_ncsr_local_group_69 0.048 r_ncsr_local_group_72 0.048 r_ncsr_local_group_136 0.048 r_ncsr_local_group_150 0.048 r_ncsr_local_group_37 0.047 r_ncsr_local_group_77 0.047 r_ncsr_local_group_99 0.047 r_ncsr_local_group_12 0.046 r_ncsr_local_group_48 0.046 r_ncsr_local_group_93 0.046 r_ncsr_local_group_97 0.046 r_ncsr_local_group_103 0.046 r_ncsr_local_group_104 0.046 r_ncsr_local_group_111 0.046 r_ncsr_local_group_137 0.046 r_ncsr_local_group_143 0.046 r_ncsr_local_group_19 0.045 r_ncsr_local_group_28 0.045 r_ncsr_local_group_38 0.045 r_ncsr_local_group_43 0.045 r_ncsr_local_group_57 0.045 r_ncsr_local_group_60 0.045 r_ncsr_local_group_91 0.045 r_ncsr_local_group_114 0.045 r_ncsr_local_group_121 0.045 r_ncsr_local_group_123 0.045 r_ncsr_local_group_125 0.045 r_ncsr_local_group_127 0.045 r_ncsr_local_group_129 0.045 r_ncsr_local_group_134 0.045 r_ncsr_local_group_138 0.045 r_ncsr_local_group_1 0.044 r_ncsr_local_group_25 0.044 r_ncsr_local_group_26 0.044 r_ncsr_local_group_31 0.044 r_ncsr_local_group_33 0.044 r_ncsr_local_group_67 0.044 r_ncsr_local_group_70 0.044 r_ncsr_local_group_73 0.044 r_ncsr_local_group_76 0.044 r_ncsr_local_group_89 0.044 r_ncsr_local_group_109 0.044 r_ncsr_local_group_118 0.044 r_ncsr_local_group_126 0.044 r_ncsr_local_group_142 0.044 r_ncsr_local_group_2 0.043 r_ncsr_local_group_8 0.043 r_ncsr_local_group_18 0.043 r_ncsr_local_group_32 0.043 r_ncsr_local_group_35 0.043 r_ncsr_local_group_46 0.043 r_ncsr_local_group_61 0.043 r_ncsr_local_group_84 0.043 r_ncsr_local_group_88 0.043 r_ncsr_local_group_116 0.043 r_ncsr_local_group_124 0.043 r_ncsr_local_group_10 0.042 r_ncsr_local_group_13 0.042 r_ncsr_local_group_15 0.042 r_ncsr_local_group_34 0.042 r_ncsr_local_group_36 0.042 r_ncsr_local_group_47 0.042 r_ncsr_local_group_50 0.042 r_ncsr_local_group_54 0.042 r_ncsr_local_group_58 0.042 r_ncsr_local_group_63 0.042 r_ncsr_local_group_74 0.042 r_ncsr_local_group_75 0.042 r_ncsr_local_group_81 0.042 r_ncsr_local_group_144 0.042 r_ncsr_local_group_151 0.042 r_ncsr_local_group_11 0.041 r_ncsr_local_group_20 0.041 r_ncsr_local_group_24 0.041 r_ncsr_local_group_39 0.041 r_ncsr_local_group_40 0.041 r_ncsr_local_group_68 0.041 r_ncsr_local_group_78 0.041 r_ncsr_local_group_82 0.041 r_ncsr_local_group_94 0.041 r_ncsr_local_group_112 0.041 r_ncsr_local_group_135 0.041 r_ncsr_local_group_152 0.041 r_ncsr_local_group_153 0.041 r_ncsr_local_group_5 0.04 r_ncsr_local_group_17 0.04 r_ncsr_local_group_21 0.04 r_ncsr_local_group_41 0.04 r_ncsr_local_group_55 0.04 r_ncsr_local_group_71 0.04 r_ncsr_local_group_96 0.04 r_ncsr_local_group_110 0.04 r_ncsr_local_group_113 0.04 r_ncsr_local_group_131 0.04 r_ncsr_local_group_139 0.04 r_ncsr_local_group_147 0.04 r_ncsr_local_group_4 0.039 r_ncsr_local_group_9 0.039 r_ncsr_local_group_49 0.039 r_ncsr_local_group_53 0.039 r_ncsr_local_group_66 0.039 r_ncsr_local_group_87 0.039 r_ncsr_local_group_117 0.039 r_symmetry_xyhbond_nbd_other 0.038 r_ncsr_local_group_3 0.038 r_ncsr_local_group_16 0.038 r_ncsr_local_group_29 0.038 r_ncsr_local_group_132 0.038 r_ncsr_local_group_145 0.038 r_ncsr_local_group_44 0.037 r_ncsr_local_group_62 0.037 r_ncsr_local_group_79 0.037 r_ncsr_local_group_85 0.037 r_ncsr_local_group_115 0.037 r_ncsr_local_group_128 0.037 r_ncsr_local_group_130 0.037 r_ncsr_local_group_141 0.035 r_ncsr_local_group_146 0.033 r_ncsr_local_group_80 0.032 r_ncsr_local_group_86 0.032 r_ncsr_local_group_83 0.028 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 48209 Nucleic Acid Atoms Solvent Atoms 1787 Heterogen Atoms 329
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing