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X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 277 1M TRIS, 5% W/V PGA-LM, 20% W/V PEG 2000 MME, pH 7.8, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.87 34.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.949 α = 90 b = 150.949 β = 90 c = 46.231 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 100 PIXEL PSI PILATUS 6M 2013-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.000 PETRA III, DESY P11
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 1.4 75.475 99.8 0.059 14.7 4.9 76922 76922 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 99 0.626 0.626 0.319 1.2 4.8 11096
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 4I2V 1.4 75.47 76922 76922 3859 99.88 0.1541 0.1541 0.1524 0.1503 0.1838 0.1825 RANDOM 18.103
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 15.922 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 5.828 r_scangle_it 2.719 r_scbond_it 1.738 r_angle_refined_deg 1.165 r_mcangle_it 1.101 r_rigid_bond_restr 0.74 r_mcbond_it 0.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 15.922 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 5.828 r_scangle_it 2.719 r_scbond_it 1.738 r_angle_refined_deg 1.165 r_mcangle_it 1.101 r_rigid_bond_restr 0.74 r_mcbond_it 0.633 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3770 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 20
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction