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Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group P1 at 2.15 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
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.703 α = 89.44 b = 123.566 β = 117.29 c = 133.238 γ = 103.2
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 PILATUS 6M 2020-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979150 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 2.15 49 89.3 0.064 0.091 0.998 6.72 3.8 344315
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 2.15 2.28 0.262 0.371 0.883
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 2.15 49 1.96 327117 16355 90.09 0.2085 0.2075 0.2076 0.2279 0.2286
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 13.012 f_angle_d 0.717 f_chiral_restr 0.051 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35361 Nucleic Acid Atoms Solvent Atoms 1588 Heterogen Atoms 186
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing