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Crystal structure of TxGH116 E730Q mutant from Thermoanaerobacterium xylanolyticum with glucose
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 0.15 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.377 α = 90 b = 124.458 β = 90 c = 174.263 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 CCD ADSC QUANTUM 315r 2020-02-26 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) 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 2.15 50.01 99.3 0.18 11.7 6.3 86926
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 2.15 2.23 0.67 0.814 2.2
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 5BVU 2.15 50.01 77195 3983 84.82 0.1551 0.1526 0.203 0.2066 RANDOM 32.49
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] -0.52 1.17 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.242 r_dihedral_angle_4_deg 20.091 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_1_deg 6.795 r_angle_refined_deg 1.577 r_angle_other_deg 0.995 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.242 r_dihedral_angle_4_deg 20.091 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_1_deg 6.795 r_angle_refined_deg 1.577 r_angle_other_deg 0.995 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12382 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building