☰ Navigation Tabs
X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RXY PDB entry 1rxy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.75M ammonium sulfate, 0.075M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP
, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.92 α = 90 b = 96.48 β = 120.01 c = 91.93 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 CCD MAR CCD 165 mm 2009-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.812 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 79.62 77.3 205488 171553 1
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 1rxy 1.6 19.49 165794 8948 95.57 0.17805 0.17729 0.176 0.19188 0.1759 RANDOM 17.451
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] -14.8 -2.94 28.87 -14.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_3_deg 15.036 r_dihedral_angle_1_deg 6.684 r_long_range_B_refined 3.35 r_angle_refined_deg 1.928 r_scbond_it 1.811 r_mcangle_it 1.79 r_mcbond_it 1.318 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_3_deg 15.036 r_dihedral_angle_1_deg 6.684 r_long_range_B_refined 3.35 r_angle_refined_deg 1.928 r_scbond_it 1.811 r_mcangle_it 1.79 r_mcbond_it 1.318 r_chiral_restr 0.136 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other 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 10850 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 93
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling