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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 1M SODIUM-ACETATE (PH 5.2), 25% PEG 4000, 0.1M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.22 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.532 α = 90 b = 77.188 β = 98.04 c = 100.878 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 100 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 1998-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.97 50 90.5 0.14 6.6 2.3 33291 1.6
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 2.97 3.08 39.6 0.44 1.7 1.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UOU 2.99 42.61 27431 926 85.2 0.207 0.207 0.284 RANDOM 29.3
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] -7.96 -2.02 -3.52 11.47
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_angle_deg 1.4 c_improper_angle_d 1.03 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 23 c_angle_deg 1.4 c_improper_angle_d 1.03 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 13010 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 6
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing