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X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M sodium acetate, pH 6.5, 17.5 % MPD with a drop size of 2 micro-liters and reservoir volume of 650 micro-liters.
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.474 α = 90 b = 109.619 β = 108.335 c = 120.782 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 PIXEL DECTRIS PILATUS 6M-F 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
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 2.95 114.65 99.6 0.073 0.079 0.999 14.2 6.8 57659 111.98
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 2.95 3.04 99.8 1.415 1.674 0.556 1 6.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.95 114.65 1.34 53315 1833 99.52 0.3458 0.3452 0.3502 0.3629 0.366 1439 127.63
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 16.0585 f_angle_d 1.3022 f_chiral_restr 0.0903 f_bond_d 0.008 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15827 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement XDS data scaling CRANK2 phasing BUCCANEER model building XDS data reduction