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Structure of e. coli uridine phosphorylase complexed to 5-(m-(benzyloxy)benzyl)acyclouridine (BBAU)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 PEG 4000, MES, GLYCEROL, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.557 α = 90 b = 125.813 β = 90 c = 141.137 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV OSMIC MULTILAYER-BLUE 2004-04-10 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) 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 99.8 72892 72892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 48.8 66733 66733 5125 98.66 0.20092 0.20092 0.19887 0.22751 0.279 RANDOM 15.917
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] -1.72 0.75 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.741 r_angle_refined_deg 0.889 r_scangle_it 0.623 r_scbond_it 0.362 r_mcangle_it 0.187 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.098 r_mcbond_it 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.741 r_angle_refined_deg 0.889 r_scangle_it 0.623 r_scbond_it 0.362 r_mcangle_it 0.187 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.099 r_symmetry_hbond_refined 0.098 r_mcbond_it 0.095 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 11178 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement MOSFLM data reduction CNS phasing