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Crystal structure of TxGH116 E441G 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 0.24 M AMMONIUM SULFATE, 20% PEG 3350, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.556 α = 90 b = 54.424 β = 90 c = 83.137 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 1.7 89 99.6 0.999 28.3 5.5 89598
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 1.7 1.76 0.911
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 1.7 88.78 84019 4344 97.88 0.1543 0.153 0.1658 0.18 0.1906 RANDOM 15.87
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] -0.08 0.18 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 6.351 r_angle_refined_deg 1.355 r_angle_other_deg 0.917 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 6.351 r_angle_refined_deg 1.355 r_angle_other_deg 0.917 r_chiral_restr 0.081 r_bond_refined_d 0.008 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 6216 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction