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uridine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2M magnesium formate, 20% PEG3350, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.71 66.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.689 α = 90 b = 185.689 β = 90 c = 50.754 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 CCD ADSC QUANTUM 270 2020-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97932 PAL/PLS 7A (6B, 6C1)
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 2.15 50 99.7 0.98 12.7 5.5 104992 52.9446533634
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 2.15 2.23 0.45
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3KZH 2.15296568597 36.8926633277 1.95835313323 104136 2002 98.2035250516 0.250970146051 0.250260285481 0.2698 0.286592009854 0.3003 93.3853131003
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.8432574571 f_angle_d 1.0288435451 f_chiral_restr 0.0411795631093 f_bond_d 0.00546262518933 f_plane_restr 0.00491648494549
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9113 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing