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Structure of the Y21F variant of quinolinate synthase in complex with PGH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.1 298 PEG33500, ammonium sulfate, oxaloacetate, DHAP, NaF, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.97 α = 90 b = 49.17 β = 107.79 c = 69.39 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 100 PIXEL DECTRIS PILATUS 6M-F 2017-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.00000 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 43.95 99.3 0.098 0.118 0.064 0.996 10.2 3.2 22406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.1 0.895 1.092 0.617 0.469 3
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 4P3X 2 39.15 21244 1156 99.19 0.1943 0.1918 0.1986 0.2414 0.2491 RANDOM 36.997
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] 0.9 0.96 -0.99 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.894 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_1_deg 5.127 r_angle_refined_deg 1.531 r_angle_other_deg 1.337 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.894 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_1_deg 5.127 r_angle_refined_deg 1.531 r_angle_other_deg 1.337 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2416 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing