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Structural features of native human thymidine phosphorylase and in complex with 5-iodouracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UOU PDB ENTRY 1UOU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.8-3.5 M SODIUM-FORMATE, 100 MM 5-IUR
Crystal Properties Matthews coefficient Solvent content 2.44 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.911 α = 90 b = 67.266 β = 90 c = 212.274 γ = 90
Symmetry Space Group P 21 21 21
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 MAR scanner 345 mm plate MIRRORS 2000-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 2.5 50 94.5 0.05 22 4.4 33589 37.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 69.6 0.18 5.9 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UOU 2.5 46.59 30049 981 95.2 0.227 0.227 0.2234 0.283 RANDOM 43.2
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] 6.09 5.82 -11.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.3 c_improper_angle_d 0.97 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.3 c_improper_angle_d 0.97 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6514 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 18
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing