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Crystal Structure of ROK family protein from Burkholderia vietnamiensis G4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Robetta ab-initio model from RobeTTA-fold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 287 RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray 269309 h7: cryio: 20% EG: puck: ocr0-5
Crystal Properties Matthews coefficient Solvent content 2.56 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.41 α = 90 b = 112.41 β = 90 c = 63.09 γ = 120
Symmetry Space Group P 31 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 RAYONIX MX-300 Beryllium Lenses 2016-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 50 99.6 0.054 0.057 1 24.05 8.413 20667 55.337
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 100 0.578 0.616 0.911 3.79 8.497
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE ab-initio model from RobeTTA-fold 2.3 48.67 1.34 20662 2184 99.69 0.2047 0.1993 0.1999 0.249 0.2493 0 62.6
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 13.4251 f_angle_d 0.8155 f_chiral_restr 0.0502 f_plane_restr 0.0074 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2660 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing