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Crystal structure of YqeK in complex with MG and ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293.15 12% 2-propannol, 18.5% PEG-4000 and 100 mM sodium HEPES (pH 7.4)
Crystal Properties Matthews coefficient Solvent content 2.55 51.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.944 α = 90 b = 37.672 β = 92.704 c = 76.301 γ = 90
Symmetry Space Group C 1 2 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 315r 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.91 35.04 98.4 0.98 3 3.7 35345 31.17
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 1.91 1.978 0.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.91 35.04 1.37 35344 1767 98.19 0.2165 0.2147 0.2155 0.2475 0.2472 35.8
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 13.8908 f_angle_d 1.5612 f_chiral_restr 0.072 f_bond_d 0.0138 f_plane_restr 0.0109
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3125 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing