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Glucose-6-phosphate 1-dehydrogenase (K403QdLtL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 295 2,2'-disulfanediylbis(N-(2-(1H-indol-3-yl)ethyl)ethan-1-amine), NADP+, MES, PEG4000, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.64 α = 90 b = 87.86 β = 90 c = 160.68 γ = 90
Symmetry Space Group P 21 21 21
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 Flat Si Rh coated Mirror 2021-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.9 38.99 99.9 0.199 0.208 0.999 13.71 13.062 24109 79.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 100 2.866 2.978 0.671 1.51 13.581
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) 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 6va7 2.9 38.99 22903 1206 99.92 0.2106 0.2058 0.2061 0.3018 0.2974 RANDOM 77.492
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] 3.85 -2.64 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_3_deg 21.517 r_dihedral_angle_4_deg 18.115 r_dihedral_angle_1_deg 8.001 r_angle_refined_deg 1.489 r_angle_other_deg 1.145 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_3_deg 21.517 r_dihedral_angle_4_deg 18.115 r_dihedral_angle_1_deg 8.001 r_angle_refined_deg 1.489 r_angle_other_deg 1.145 r_chiral_restr 0.063 r_bond_refined_d 0.005 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 7158 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 96
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing