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E. coli uridine phosphorylase: type-B native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGG TYPE-A NATIVE (1LGG)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 TRIS HCL, PEG4000, POTASSIUM ACETATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.25 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.928 α = 90 b = 152.928 β = 90 c = 50.864 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 110 CCD ADSC QUANTUM 4 1999-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.10 NSLS X26C
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 1.7 16.54 99.9 0.053 9.7 5.4 48715 48715 21.544
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 1.7 1.79 99.9 0.337 2.2 5.1 7095
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 (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 TYPE-A NATIVE (1LGG) 1.7 16.1 46224 46224 2478 99.98 0.13002 0.12819 0.1423 0.16442 0.1749 RANDOM 12.299
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.944 r_scangle_it 2.334 r_scbond_it 1.562 r_angle_refined_deg 1.547 r_angle_other_deg 1.264 r_mcangle_it 1.109 r_mcbond_it 0.683 r_symmetry_vdw_other 0.312 r_nbd_other 0.235 r_nbd_refined 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.944 r_scangle_it 2.334 r_scbond_it 1.562 r_angle_refined_deg 1.547 r_angle_other_deg 1.264 r_mcangle_it 1.109 r_mcbond_it 0.683 r_symmetry_vdw_other 0.312 r_nbd_other 0.235 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.209 r_chiral_restr 0.168 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.098 r_nbtor_other 0.078 r_metal_ion_refined 0.031 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other 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 3703 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 28
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling