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Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group I212121 at 2.65 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other WT SAD Structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1 M ammonium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, 0.1 M praseodyminium
Crystal Properties Matthews coefficient Solvent content 3.21 61.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.853 α = 90 b = 192.001 β = 90 c = 191.921 γ = 90
Symmetry Space Group I 21 21 21
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 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979340 SSRL BL9-2
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 2.65 48 99.7 0.163 0.176 0.989 4.6 7.06 102548
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 2.65 2.81 1.361 1.916 0.244
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 2.65 45.25 1.34 102256 5115 99.75 0.2041 0.2026 0.2026 0.2329 0.2329
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 13.907 f_angle_d 0.763 f_chiral_restr 0.055 f_plane_restr 0.012 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17752 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 176
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing