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Structure of quinolinate synthase in complex with 5-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, HANGING DROP 6.7 298 PEG33500, dioxane, Na2HPO4, MES, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.9 α = 90 b = 48.5 β = 107.1 c = 60.5 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 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.00394 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 2.1 37.16 95.3 0.143 0.171 0.091 0.982 8.5 3 17011
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 2.1 2.17 96.7 0.887 1.064 0.576 0.536 2.9
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 2.1 37.16 16177 830 94.69 0.1999 0.1978 0.205 0.2393 0.2494 RANDOM 43.712
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] -0.82 -0.77 0.18 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 16.413 r_dihedral_angle_1_deg 5.499 r_angle_other_deg 1.558 r_angle_refined_deg 1.543 r_chiral_restr 0.105 r_bond_other_d 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 16.413 r_dihedral_angle_1_deg 5.499 r_angle_other_deg 1.558 r_angle_refined_deg 1.543 r_chiral_restr 0.105 r_bond_other_d 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2397 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction