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Crystal structure of TxGH116 from Thermoanaerobacterium xylanolyticum with isofagomine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLOLYTICUM GH116 BETA-GLUCOSIDASE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 0.2 M AMMONIUM SULFATE, 23% PEG 3000, 0.1 M MES, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.2 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.791 α = 90 b = 164.399 β = 90 c = 179.614 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 RAYONIX MX300HE 2015-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 50.01 98.8 0.114 26.7 6.4 109281
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 2.03 94.5 0.447 0.884 5.2 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 50.01 103720 5466 98.45 0.1569 0.155 0.1677 0.193 0.2033 RANDOM 22.149
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] 1.38 -0.62 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.234 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_1_deg 6.47 r_angle_refined_deg 1.491 r_angle_other_deg 0.987 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.234 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_1_deg 6.47 r_angle_refined_deg 1.491 r_angle_other_deg 0.987 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12434 Nucleic Acid Atoms Solvent Atoms 967 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building