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Structure of quinolinate synthase Y21F mutant in complex with substrate-derived quinolinate
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 298 PEG3350, ammonium sulfate, oxaloacetate, DHAP, NaCl, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.06 α = 90 b = 48.74 β = 103.67 c = 60.25 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 CCD ADSC QUANTUM 315r 2015-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979736 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 43.73 98.6 0.094 0.989 15.2 3.6 23026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.8 0.588 0.551 2.9 3.6
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 1.9 40 21850 1175 98.58 0.17792 0.17594 0.1827 0.21439 0.2154 RANDOM 21.143
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] 0.37 -0.3 -0.3 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.833 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.553 r_long_range_B_refined 6.234 r_long_range_B_other 5.974 r_dihedral_angle_1_deg 5.64 r_scangle_other 3.182 r_mcangle_other 2.222 r_mcangle_it 2.213 r_scbond_it 1.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.833 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.553 r_long_range_B_refined 6.234 r_long_range_B_other 5.974 r_dihedral_angle_1_deg 5.64 r_scangle_other 3.182 r_mcangle_other 2.222 r_mcangle_it 2.213 r_scbond_it 1.931 r_scbond_other 1.931 r_angle_refined_deg 1.574 r_mcbond_it 1.4 r_mcbond_other 1.399 r_angle_other_deg 1.085 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2401 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing