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Crystal structure of human uridine phosphorylase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EUE PDB ENTRY 3EUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.2 MGCL2, 0.1 M TRIS PH 8, 25% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.4 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.28 α = 90 b = 95.28 β = 90 c = 186.28 γ = 120
Symmetry Space Group P 31 2 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 CCD MARMOSAIC 225 mm CCD DOUBLE CRYSTAL MONOCHROMATOR 2010-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 34.4 99.7 0.14 18.1 11.2 44181 2 28
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 2.3 2.36 100 0.53 5.3 11.3
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 3EUE 2.3 33.67 44177 2230 0.1697 0.1677 0.1639 0.2065 0.1678 RANDOM 22.82
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] -2.0567 -2.0567 4.1134
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.13 t_other_torsion 2.66 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.13 t_other_torsion 2.66 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6734 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 45
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing