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Crystal structure of E.coli uridine phosphorylase at 2.2 A resolution (Type-A Native)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Tris-HCl, PEG, Sodium Acetate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.336 α = 90 b = 151.336 β = 90 c = 48.366 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 IMAGE PLATE MARRESEARCH 1998-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 29.11 99.8 0.086 15.08 3.77 188478 20914 0.5 25.5
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 2.2 2.28 100 0.281 4.42 3.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SIR(URANYL DERIVATIVE) THROUGHOUT 2.2 29.11 20914 19837 1075 99.8 0.163 0.163 0.161 0.1692 0.203 0.2061 RANDOM 20.73
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] -0.51 -0.25 -0.51 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.404 r_scangle_it 4.624 r_dihedral_angle_1_deg 4.156 r_scbond_it 2.795 r_angle_refined_deg 1.831 r_mcangle_it 1.79 r_angle_other_deg 1.452 r_mcbond_it 0.97 r_symmetry_vdw_other 0.342 r_symmetry_vdw_refined 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.404 r_scangle_it 4.624 r_dihedral_angle_1_deg 4.156 r_scbond_it 2.795 r_angle_refined_deg 1.831 r_mcangle_it 1.79 r_angle_other_deg 1.452 r_mcbond_it 0.97 r_symmetry_vdw_other 0.342 r_symmetry_vdw_refined 0.258 r_nbd_other 0.237 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.116 r_xyhbond_nbd_other 0.111 r_nbtor_other 0.05 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 3511 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing REFMAC refinement