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Crystal structure at 1.9A of the apo quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 20% PEG 3350, 0.2 M ammonium formate; holo-quinolinate: 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 = 154.913 α = 90 b = 154.913 β = 90 c = 68.946 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979126 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 1.9 30 94.9 0.064 0.064 17.8 9 25007 23727 1 1 44.4
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) 1.9 1.97 72.5 0.31 0.31 2.98 4.9 1810
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1.9 28.1 2 21799 1109 91.87 0.235 0.234 0.236 0.259 0.2631 RANDOM 44.407
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] -2.82 -1.41 -2.82 4.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.556 r_dihedral_angle_4_deg 22.57 r_scangle_it 18.712 r_dihedral_angle_3_deg 15.839 r_scbond_it 15.171 r_mcangle_it 10.494 r_mcbond_it 8.803 r_dihedral_angle_1_deg 1.306 r_angle_refined_deg 1.288 r_symmetry_hbond_refined 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.556 r_dihedral_angle_4_deg 22.57 r_scangle_it 18.712 r_dihedral_angle_3_deg 15.839 r_scbond_it 15.171 r_mcangle_it 10.494 r_mcbond_it 8.803 r_dihedral_angle_1_deg 1.306 r_angle_refined_deg 1.288 r_symmetry_hbond_refined 0.354 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.284 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.097 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling