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Co-crystal structure of Chaetomium glucosidase with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J5T
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 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.839 α = 90 b = 178.544 β = 90 c = 179.806 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 1.9 46.77 99.35 0.1458 0.061 0.996 9.98 6.5 168664 30.61
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 1.905 1.973 95.82 1.791 0.7917 0.407 0.98 5.8
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 4J5T 1.905 46.77 160292 8369 99.4 0.1761 0.1743 0.1745 0.2124 0.212 RANDOM 33.638
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] 1.46 0.24 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.475 r_dihedral_angle_4_deg 17.129 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_1_deg 6.609 r_angle_refined_deg 1.499 r_chiral_restr 0.114 r_gen_planes_refined 0.011 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12148 Nucleic Acid Atoms Solvent Atoms 1269 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing