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Crystal structure of ligand-free human uridine phosphorylase 1 (hUPP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1C PDB ENTRY 1U1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.2M Ammonium sulfate, 1% MPD, 100 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.72 73.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.777 α = 90 b = 253.777 β = 90 c = 253.777 γ = 90
Symmetry Space Group F 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2008-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.00000 SSRL BL9-1
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 50 99.9 0.072 30.7 11.3 31750 31733
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) 2.3 2.38 99.7 0.384 5.72
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 1U1C 2.3 50 30108 1601 99.87 0.20468 0.20378 0.2009 0.22099 0.216 RANDOM 46.487
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 r_dihedral_angle_2_deg 38.103 r_dihedral_angle_4_deg 22.606 r_dihedral_angle_3_deg 14.542 r_dihedral_angle_1_deg 6.462 r_scangle_it 4.713 r_scbond_it 3.127 r_mcangle_it 1.968 r_angle_refined_deg 1.675 r_mcbond_it 1.235 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.103 r_dihedral_angle_4_deg 22.606 r_dihedral_angle_3_deg 14.542 r_dihedral_angle_1_deg 6.462 r_scangle_it 4.713 r_scbond_it 3.127 r_mcangle_it 1.968 r_angle_refined_deg 1.675 r_mcbond_it 1.235 r_nbtor_refined 0.305 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2267 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 6
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling