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X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.848 α = 90 b = 96.715 β = 119.96 c = 92.89 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 PIXEL PSI PILATUS 6M 2015-05-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.97989 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 1.06 46.461 95.6 0.066 16.26 6.5 615831 -3 11.28
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 1.06 1.12 83.7 0.608 2.54
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 4K6O 1.06 46.46 585343 30490 95.7 0.106 0.105 0.1071 0.122 0.124 RANDOM 11.75
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] -0.39 -0.26 0.94 -0.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.454 r_dihedral_angle_2_deg 29.286 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 12.223 r_sphericity_bonded 9.785 r_dihedral_angle_1_deg 6.005 r_rigid_bond_restr 3.736 r_mcangle_it 1.633 r_angle_refined_deg 1.504 r_mcbond_it 1.229
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.454 r_dihedral_angle_2_deg 29.286 r_dihedral_angle_4_deg 18.518 r_dihedral_angle_3_deg 12.223 r_sphericity_bonded 9.785 r_dihedral_angle_1_deg 6.005 r_rigid_bond_restr 3.736 r_mcangle_it 1.633 r_angle_refined_deg 1.504 r_mcbond_it 1.229 r_mcbond_other 1.228 r_angle_other_deg 0.974 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2) r_scbond_it SIDE-CHAIN BOND OTHER ATOMS (A**2) r_scangle_it SIDE-CHAIN ANGLE OTHER ATOMS (A**2) LONG RANGE B REFINED ATOMS (A**2) LONG RANGE B OTHER ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11299 Nucleic Acid Atoms Solvent Atoms 2207 Heterogen Atoms 306
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing