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E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other DETWINNED HEXAMERIC NATIVE UP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH METHOD UNDER OIL 7.5 289 TRIS HCL, PEG4000, POTASSIUM ACETATE, 2'-DEOXYURIDINE, SODIUM ORTHOVANADATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.25 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.958 α = 90 b = 98.212 β = 109.09 c = 242.729 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 115 IMAGE PLATE MARRESEARCH OSMIC 2002-08-05 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 2.8 40.49 97.8 0.123 5.4 3.1 173525 173525 46.18
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 2.8 2.94 95.3 0.413 1.8 3.1 19170
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT DETWINNED HEXAMERIC NATIVE UP 2.8 26.75 166227 166227 8725 99.16 0.17794 0.17794 0.17585 0.177 0.21814 0.2163 RANDOM 17.286
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] -0.11 0.1 0.91 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.995 r_scangle_it 3.011 r_scbond_it 1.639 r_angle_refined_deg 1.362 r_mcangle_it 0.966 r_symmetry_vdw_refined 0.552 r_symmetry_hbond_refined 0.521 r_mcbond_it 0.474 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.995 r_scangle_it 3.011 r_scbond_it 1.639 r_angle_refined_deg 1.362 r_mcangle_it 0.966 r_symmetry_vdw_refined 0.552 r_symmetry_hbond_refined 0.521 r_mcbond_it 0.474 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.088 r_metal_ion_refined 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 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_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 55267 Nucleic Acid Atoms Solvent Atoms 1581 Heterogen Atoms 760
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling