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THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.1 M MES PH 6.0-6.2 25% PEG 6000 PSEUDOURIDINE AT 10X PROTEIN CONCENTRATION
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.57 α = 90 b = 70.45 β = 98.02 c = 122.78 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 108 CCD ADSC 1997-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 2 30 88.4 0.067 2.9 55716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2TPT 2.1 30 2 54378 2431 82.9 0.232 0.232 0.276 0.3017 RANDOM 26.9
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 22.6 x_angle_deg 1.2 x_improper_angle_d 1.2 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 22.6 x_angle_deg 1.2 x_improper_angle_d 1.2 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6438 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 44
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing