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Glucose-6-phosphate 1-dehydrogenase (K403Q)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 PEG8K
Crystal Properties Matthews coefficient Solvent content 5.96 79.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.73 α = 90 b = 157.73 β = 90 c = 113.82 γ = 90
Symmetry Space Group P 41 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 EIGER X 16M Flat side-deflecting, Rh-coated Si mirror 2021-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
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 3.65 39.43 99.9 0.213 0.217 0.999 15.3 26.588 16483 120.317
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 3.65 3.74 100 2.745 2.796 0.632 1.65 27.375
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 6va8 3.65 39.43 15658 825 99.87 0.1935 0.1913 0.1935 0.2352 0.2398 RANDOM 138.286
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.153 r_dihedral_angle_3_deg 20.193 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_1_deg 8.735 r_angle_refined_deg 1.733 r_angle_other_deg 1.222 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.153 r_dihedral_angle_3_deg 20.193 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_1_deg 8.735 r_angle_refined_deg 1.733 r_angle_other_deg 1.222 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3439 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing