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Mutant D24G of uridine phosphorylase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Potassium citrate tribasic monohydrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.88 34.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.07 α = 90 b = 150.07 β = 90 c = 46.36 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 100 PIXEL DECTRIS PILATUS 6M 2018-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9537 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.68 30 100 1 9.9 7.3 44388
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 0.58
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4R2X 1.7 30 42872 2155 99.967 0.156 0.154 0.1631 0.2021 0.2097 28.629
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] -0.124 -0.062 -0.124 0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 23.276 r_dihedral_angle_3_deg 14.566 r_dihedral_angle_1_deg 7.151 r_lrange_it 5.946 r_scangle_it 5.707 r_scbond_it 4.29 r_mcangle_it 2.876 r_mcbond_it 2.352 r_angle_refined_deg 2.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_4_deg 23.276 r_dihedral_angle_3_deg 14.566 r_dihedral_angle_1_deg 7.151 r_lrange_it 5.946 r_scangle_it 5.707 r_scbond_it 4.29 r_mcangle_it 2.876 r_mcbond_it 2.352 r_angle_refined_deg 2.103 r_nbtor_refined 0.308 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.207 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.137 r_symmetry_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3752 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing