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Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with cellobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 0.16 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.259 α = 90 b = 54.459 β = 90 c = 83.154 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315r 2018-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 1.6 89 98.2 0.999 50.9 6.7 105220
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 1.6 1.66 91 0.973
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 5BVU 1.6 88.63 99857 5170 98.14 0.1568 0.1556 0.1687 0.1797 0.1901 RANDOM 14.986
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] -0.05 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 18.724 r_dihedral_angle_3_deg 11.514 r_dihedral_angle_1_deg 6.224 r_angle_refined_deg 1.314 r_angle_other_deg 0.914 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 18.724 r_dihedral_angle_3_deg 11.514 r_dihedral_angle_1_deg 6.224 r_angle_refined_deg 1.314 r_angle_other_deg 0.914 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6217 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction