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Structure of Uracil phosphoribosyl transferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 295 0.05M MES, 1.5M NH2SO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.08 60.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.312 α = 90 b = 91.312 β = 90 c = 266.911 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU GRAPHITE 2006-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.8 40 99.9 0.097 6.3 6.4 28689 28400 58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.8
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 (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 1V9S 2.8 20 28689 26956 1447 99.01 0.21 0.21 0.21 0.229 0.2529 RANDOM 53.382
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] 1.65 1.65 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.273 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 15.679 r_scangle_it 6.071 r_scbond_it 3.571 r_mcangle_it 2.195 r_angle_refined_deg 1.388 r_mcbond_it 1.267 r_dihedral_angle_1_deg 1.232 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.273 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 15.679 r_scangle_it 6.071 r_scbond_it 3.571 r_mcangle_it 2.195 r_angle_refined_deg 1.388 r_mcbond_it 1.267 r_dihedral_angle_1_deg 1.232 r_nbtor_refined 0.333 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.27 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6324 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing