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Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold ALPHAFOLD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 100 mM MES, 30% PEG 8000, 5% GLYCEROLE
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.09 α = 90 b = 108.74 β = 90 c = 251.27 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 S 16M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 98.7 0.057 15.5 4.7 269815
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 0.514 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT ALPHAFOLD2 1.7 30 256285 13488 98.68 0.1275 0.1261 0.1534 0.1613 RANDOM 22.72
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] -0.25 0.35 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.92 r_dihedral_angle_4_deg 13.77 r_dihedral_angle_3_deg 11.657 r_dihedral_angle_1_deg 7.645 r_angle_refined_deg 1.2 r_angle_other_deg 1.197 r_rigid_bond_restr 0.583 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.92 r_dihedral_angle_4_deg 13.77 r_dihedral_angle_3_deg 11.657 r_dihedral_angle_1_deg 7.645 r_angle_refined_deg 1.2 r_angle_other_deg 1.197 r_rigid_bond_restr 0.583 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15561 Nucleic Acid Atoms Solvent Atoms 2088 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction X-Area data reduction XSCALE data scaling REFMAC phasing