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Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with alpha-glucosyl fluoride
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 0.14 M AMMONIUM SULFATE, 21% PEG 3350, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.049 α = 90 b = 54.689 β = 90 c = 83.24 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 RAYONIX MX300HE 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.65 89 99.6 0.985 5.1 7.5 97660
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 1.65 1.68 99.1 0.83 7.5
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 1.65 88.52 90318 4685 96.84 0.1616 0.1602 0.1873 0.212 RANDOM 16.882
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] -0.23 0.35 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.475 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_3_deg 11.981 r_dihedral_angle_1_deg 6.264 r_angle_refined_deg 1.344 r_angle_other_deg 0.917 r_chiral_restr 0.083 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 36.475 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_3_deg 11.981 r_dihedral_angle_1_deg 6.264 r_angle_refined_deg 1.344 r_angle_other_deg 0.917 r_chiral_restr 0.083 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 6217 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction