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Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 3350, 0.2 M ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.668 α = 90 b = 154.668 β = 90 c = 69.346 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD BRUKER SMART 2000 2005-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 50 99.2 0.083 0.083 3.95 4.6 14205 14089 1 1 50.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 98.4 0.39 0.39 3.95 4 1388
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.29 44.63 12818 514 90.99 0.227 0.225 0.2337 0.282 0.3025 RANDOM 50.579
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] -5.24 -2.62 -5.24 7.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.358 r_dihedral_angle_4_deg 19.919 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_1_deg 12.026 r_scangle_it 3.093 r_scbond_it 2.131 r_mcangle_it 1.704 r_angle_refined_deg 1.675 r_mcbond_it 0.983 r_chiral_restr 0.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.358 r_dihedral_angle_4_deg 19.919 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_1_deg 12.026 r_scangle_it 3.093 r_scbond_it 2.131 r_mcangle_it 1.704 r_angle_refined_deg 1.675 r_mcbond_it 0.983 r_chiral_restr 0.578 r_nbtor_refined 0.336 r_nbd_refined 0.313 r_symmetry_hbond_refined 0.282 r_symmetry_vdw_refined 0.268 r_xyhbond_nbd_refined 0.196 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2067 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction