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The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JBM PDB ENTRY 2JBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 50 mM MES, pH 6.5, 0.1 M sodium phosphate monobasic, 0.1 M potassium phosphate monobasic, 1.6-2.1 M sodium chloride, 4 mM phthalic acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.03 59.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.837 α = 90 b = 179.837 β = 90 c = 121.371 γ = 120
Symmetry Space Group P 32 2 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 2012-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9795 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.55 155.8 99.8 0.168 16.6 18.5 73606 73606 -3
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 2.55 2.59 99.3 0.864 3.7 18.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2JBM 2.55 155.74 73606 69874 3708 99.72 0.19664 0.19664 0.19483 0.1931 0.23086 0.228 RANDOM 30.864
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] 0.34 0.17 0.34 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.113 r_dihedral_angle_4_deg 18.473 r_dihedral_angle_3_deg 15.939 r_dihedral_angle_1_deg 5.392 r_angle_refined_deg 1.629 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12171 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 72
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling