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Crystal structure of GH11 from Thermoanaerobacterium saccharolyticum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 4.0 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.113 α = 90 b = 73.113 β = 90 c = 165.425 γ = 90
Symmetry Space Group P 43 21 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 2020-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 50 99.5 0.999 37.22 19.1 72944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.624
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 AlphaFold 1.5 49.39 70594 1993 99.95 0.15967 0.15897 0.1592 0.18515 0.1857 RANDOM 19.8
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] 0.24 0.24 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 17.824 r_dihedral_angle_3_deg 10.856 r_dihedral_angle_1_deg 8.2 r_long_range_B_refined 5.336 r_long_range_B_other 4.801 r_scangle_other 3.344 r_scbond_it 2.369 r_scbond_other 2.369 r_mcangle_it 2.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.042 r_dihedral_angle_4_deg 17.824 r_dihedral_angle_3_deg 10.856 r_dihedral_angle_1_deg 8.2 r_long_range_B_refined 5.336 r_long_range_B_other 4.801 r_scangle_other 3.344 r_scbond_it 2.369 r_scbond_other 2.369 r_mcangle_it 2.158 r_mcangle_other 2.158 r_angle_refined_deg 1.811 r_mcbond_it 1.667 r_mcbond_other 1.664 r_angle_other_deg 1.609 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2850 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing