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Co-crystal structure of Chaetomium glucosidase with compound 17
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 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.261 α = 90 b = 180.007 β = 90 c = 180.434 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 PILATUS3 6M 2021-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9793 APS 23-ID-D
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 2.15 46.95 99.86 0.109 0.045 0.994 16.8 6.6 118557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 98.86 0.528 0.565 1.08 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7T6W 2.15 46.95 112727 5830 99.87 0.1945 0.1924 0.1974 0.2361 0.2391 RANDOM 42.934
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] -0.56 1.58 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.639 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 15.882 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.507 r_angle_other_deg 1.307 r_chiral_restr 0.073 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.639 r_dihedral_angle_4_deg 18.12 r_dihedral_angle_3_deg 15.882 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.507 r_angle_other_deg 1.307 r_chiral_restr 0.073 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12150 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing