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Structure of the Y21F variant of quinolinate synthase in complex with phthalate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P3X 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM) experimental model PDB 5LQM 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 PEG3350, TRIS, KCL, HEPES, PHTHALATE, Na2HPO4, ANAEROBIC
Crystal Properties Matthews coefficient Solvent content 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.14 α = 103.82 b = 52.16 β = 90.63 c = 58.95 γ = 90.37
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 2017-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 49.13 90.2 0.056 0.072 0.044 0.996 12.1 2.4 34665
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 91.9 0.276 0.353 0.217 0.898 2.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM) 2 43.43 32832 1831 90.22 0.1919 0.1896 0.1966 0.2338 0.2389 RANDOM 31.326
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] -0.15 -0.02 -0.47 1.25 -1.95 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 5.253 r_angle_other_deg 1.923 r_angle_refined_deg 1.447 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 5.253 r_angle_other_deg 1.923 r_angle_refined_deg 1.447 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4811 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction