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Co-crystal structure of Chaetomium glucosidase with compound 23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 0.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.653 α = 90 b = 177.198 β = 90 c = 180.176 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 16M 2021-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 46.8 97.51 0.08747 0.0312 0.997 13.97 8.8 96056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 92.96 0.5998 0.2078 0.916 2.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7T6W 2.3 46.8 91349 4698 99.01 0.1998 0.1975 0.2463 0.2361 RANDOM 43.007
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] 2.43 0.19 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 17.631 r_dihedral_angle_3_deg 16.527 r_dihedral_angle_1_deg 7.557 r_angle_refined_deg 1.592 r_angle_other_deg 1.335 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 17.631 r_dihedral_angle_3_deg 16.527 r_dihedral_angle_1_deg 7.557 r_angle_refined_deg 1.592 r_angle_other_deg 1.335 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12024 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing