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Pseudouridine 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 295 0.1M lithium chloride, 0.1M MES (pH6.0), 18% PEG 6,000
Crystal Properties Matthews coefficient Solvent content 3.42 64.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.954 α = 90 b = 271.889 β = 110.909 c = 101.202 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 100 CCD ADSC QUANTUM 270 2020-11-11 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 2.75 50 99.7 0.954 7.75 3.5 92181 52.7690986986
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 2.75 2.85 0.342
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 2.75029193467 33.6410688561 1.33632185377 92053 1993 98.1856774111 0.29677572334 0.296140865622 0.3019 0.324860804975 0.3272 69.0481354329
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 16.1657157394 f_angle_d 0.801961302585 f_chiral_restr 0.0326037726708 f_bond_d 0.00348375524396 f_plane_restr 0.0033521381491
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15659 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing