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Structure of quinolinate synthase in complex with citrate
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, HANGING DROP 5.4 298 PEG4000, Na3citrate, NH4acetate, NaCl, anaerobic
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.948 α = 90 b = 49.3 β = 104.25 c = 62.701 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 PILATUS 6M-F 2015-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.57 49.3 99.1 0.1 9.5 5.5 40043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.62 99.1 0.841 1.5 5.1
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 1.6 27.77 36433 1896 99.79 0.13038 0.12793 0.1299 0.17701 0.1777 RANDOM 20.114
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] 0.64 -0.6 -0.25 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_sphericity_free 31.092 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 13.505 r_sphericity_bonded 10.26 r_dihedral_angle_1_deg 5.176 r_long_range_B_refined 4.406 r_long_range_B_other 4.014 r_scangle_other 3.206 r_scbond_other 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_sphericity_free 31.092 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 13.505 r_sphericity_bonded 10.26 r_dihedral_angle_1_deg 5.176 r_long_range_B_refined 4.406 r_long_range_B_other 4.014 r_scangle_other 3.206 r_scbond_other 2.611 r_scbond_it 2.61 r_mcangle_other 2.411 r_mcangle_it 2.41 r_mcbond_other 1.802 r_mcbond_it 1.801 r_rigid_bond_restr 1.629 r_angle_refined_deg 1.557 r_angle_other_deg 1.011 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2402 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing