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Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design
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 7 20% GLYCEROL, 20% PEG3350, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.04 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.078 α = 90 b = 76.087 β = 98.61 c = 99.575 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 MARRESEARCH 2005-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MAR345
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 2.3 30 99.3 0.12 18.2 8.6 63091 2
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 2.3 2.38 99 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UOU 2.31 102.06 63091 3368 99.3 0.248 0.246 0.2892 0.287 0.3201 RANDOM 12.84
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] -2.52 0.3 -1.2 3.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_1_deg 5.518 r_scangle_it 5.404 r_scbond_it 2.888 r_mcangle_it 1.461 r_angle_refined_deg 1.247 r_mcbond_it 0.829 r_symmetry_hbond_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_1_deg 5.518 r_scangle_it 5.404 r_scbond_it 2.888 r_mcangle_it 1.461 r_angle_refined_deg 1.247 r_mcbond_it 0.829 r_symmetry_hbond_refined 0.362 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.292 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13036 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing