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Structure of quinolinate synthase with reaction intermediates X and Y
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, Bis Tris propane, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.29 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.5 α = 90 b = 48.95 β = 107.27 c = 61.25 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 EIGER X 4M 2016-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.5 37.54 98.8 0.052 0.059 0.028 0.998 16.8 4.4 49728
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 1.5 1.55 99.3 0.907 1.032 0.488 0.719 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P3X 1.5 37.5 47225 2499 98.62 0.1365 0.1343 0.1789 0.1841 RANDOM 27.231
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] 2.21 -1.27 -1.34 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.486 r_sphericity_free 27.255 r_dihedral_angle_4_deg 17.547 r_sphericity_bonded 13.535 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 5.22 r_rigid_bond_restr 1.75 r_angle_refined_deg 1.497 r_angle_other_deg 1.142 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.486 r_sphericity_free 27.255 r_dihedral_angle_4_deg 17.547 r_sphericity_bonded 13.535 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 5.22 r_rigid_bond_restr 1.75 r_angle_refined_deg 1.497 r_angle_other_deg 1.142 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2387 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing