☰ Navigation Tabs
Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P1 at 2.25 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 0.75 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.22 61.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.978 α = 89.21 b = 124.405 β = 117.47 c = 133.484 γ = 103.29
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 2M 2020-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 1.369990 LNLS SIRIUS MANACA
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 2.25 48.39 95.2 0.091 0.108 0.994 4.71 3.51 312213
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 2.25 2.39 1.17 1.017 0.233
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 2.25 47.41 1.96 312107 15609 96.78 0.2318 0.2303 0.2303 0.2597 0.2593
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 12.6 f_angle_d 0.538 f_chiral_restr 0.044 f_plane_restr 0.006 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34860 Nucleic Acid Atoms Solvent Atoms 1156 Heterogen Atoms 338
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing