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Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Sachharomyces cerevisiae complexed with quinolinate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 20% PEG 3000, 0.1 M citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.802 α = 90 b = 154.802 β = 90 c = 68.621 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 MARMOSAIC 225 mm CCD 2005-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.88557 SSRL BL9-2
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 30 100 0.094 0.094 16.7 11.1 14088 14088 1 1 36.6
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 2.36 100 0.396 0.396 5.4 10.8 1029
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 2.3 29.26 13774 559 97.8 0.207 0.206 0.2058 0.237 0.2392 RANDOM 36.601
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] -3.24 -1.62 -3.24 4.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.293 r_dihedral_angle_4_deg 23.69 r_scangle_it 18.087 r_scbond_it 15.389 r_dihedral_angle_3_deg 14.959 r_mcangle_it 11.305 r_mcbond_it 9.583 r_dihedral_angle_1_deg 9.025 r_angle_other_deg 4.309 r_mcbond_other 3.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.293 r_dihedral_angle_4_deg 23.69 r_scangle_it 18.087 r_scbond_it 15.389 r_dihedral_angle_3_deg 14.959 r_mcangle_it 11.305 r_mcbond_it 9.583 r_dihedral_angle_1_deg 9.025 r_angle_other_deg 4.309 r_mcbond_other 3.606 r_angle_refined_deg 1.756 r_xyhbond_nbd_refined 0.352 r_symmetry_hbond_refined 0.315 r_symmetry_vdw_other 0.298 r_nbd_other 0.297 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.216 r_nbtor_refined 0.198 r_chiral_restr 0.165 r_nbtor_other 0.12 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2023 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection