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Crystal structure of the complex of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27 with S-1,2-Propanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M NaCl, 0.16M MgCl2, 0.05M Tris HCl pH 8.5, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55 α = 90 b = 75.73 β = 90 c = 176.6 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 IMAGE PLATE MAR scanner 345 mm plate 2016-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.26 32.01 99.7 0.121 0.131 0.049 0.994 11.7 6.9 35363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.33 97.2 0.445 0.485 0.19 0.96 6.3
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 2F8Q 2.26 30.01 33198 1730 98.61 0.1899 0.188 0.1963 0.2271 0.2308 RANDOM 22.096
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] 0.48 1.64 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 15.442 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_1_deg 6.207 r_angle_refined_deg 1.602 r_angle_other_deg 1.029 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.403 r_dihedral_angle_4_deg 15.442 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_1_deg 6.207 r_angle_refined_deg 1.602 r_angle_other_deg 1.029 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5759 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction SCALA data reduction PHASER phasing