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Structure of quinolinate synthase in complex with 6-mercaptopyridine-2,3-dicarboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.3 298 PEG33500, dioxane, Na2HPO4, HEPES, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.5 α = 90 b = 48.7 β = 107 c = 60.6 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 S 6M 2017-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 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 1.9 46.49 99.7 0.125 0.137 0.055 0.995 9 5.8 24522
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 1.9 1.97 99.7 1.133 1.263 0.545 0.573 5.2
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 6F48 1.9 46.49 23281 1227 99.55 0.1714 0.1699 0.1755 0.2003 0.2031 RANDOM 34.929
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] 0.04 -1.22 -0.19 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.537 r_angle_other_deg 1.51 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_bond_other_d 0.011 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.537 r_angle_other_deg 1.51 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_bond_other_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2382 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing