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Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400
Crystal Properties Matthews coefficient Solvent content 4.93 75.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 230.11 α = 90 b = 230.11 β = 90 c = 230.11 γ = 90
Symmetry Space Group P 41 3 2
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 PILATUS3 X 6M 2016-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3 72.8 100 0.137 0.139 0.027 0.999 28.9 26 42107 44.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 99.1 0.524 0.534 0.105 0.974 7.5 7.5
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 SAD FREE R-VALUE 3 69.38 1.34 42037 2129 99.89 0.1551 0.1534 0.1579 0.1861 0.1845 40.3
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 13.9408 f_angle_d 0.5645 f_chiral_restr 0.0427 f_plane_restr 0.0045 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7177 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 207
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling HKL-3000 phasing MLPHARE phasing