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Glycoside hydrolase family 81 from Clostridium thermocellum (CtLam81A), Mutant E515A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 30% (w/v) 2-methyl-2,4-pentanediol, 0.1M sodium acetate pH4,6 and 0.02M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.917 α = 90 b = 139.033 β = 90 c = 197.909 γ = 90
Symmetry Space Group I 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 PILATUS 6M-F 2016-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9919 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 45.15 99.5 0.066 0.998 14.7 6.6 166379
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 99 0.608 0.904 6.9
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 4K3A 1.4 45.15 158020 8356 99.37 0.1089 0.1077 0.1078 0.1327 0.1323 RANDOM 19.355
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] 1.36 -0.48 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.419 r_sphericity_free 31.595 r_dihedral_angle_4_deg 11.692 r_dihedral_angle_3_deg 10.593 r_sphericity_bonded 10.287 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 1.625 r_angle_refined_deg 1.481 r_angle_other_deg 0.959 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.419 r_sphericity_free 31.595 r_dihedral_angle_4_deg 11.692 r_dihedral_angle_3_deg 10.593 r_sphericity_bonded 10.287 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 1.625 r_angle_refined_deg 1.481 r_angle_other_deg 0.959 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5660 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing