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Crystal structure of aromatic mutant (F4W) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
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 MICROBATCH 8.5 293 0.1M NaCl, 120mM MgCl2, 0.1M Tris-HCl pH 8.5, 18% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.3 46.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.27 α = 90 b = 77.32 β = 90 c = 176.75 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 RIGAKU 2012-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.219 88.375 98.4 0.083 0.089 0.033 15.1 7.1 38071 38071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.33 89.8 0.2 0.2 0.081 3.7 6.7 4956
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 2F8Q 2.22 88.375 36158 1841 99.08 0.1706 0.1684 0.2139 0.2133 RANDOM 27.172
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] 2.74 1.43 -4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.03 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 12.301 r_dihedral_angle_1_deg 5.786 r_mcangle_it 1.503 r_angle_refined_deg 1.228 r_mcbond_it 0.911 r_mcbond_other 0.911 r_angle_other_deg 0.783 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.03 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 12.301 r_dihedral_angle_1_deg 5.786 r_mcangle_it 1.503 r_angle_refined_deg 1.228 r_mcbond_it 0.911 r_mcbond_other 0.911 r_angle_other_deg 0.783 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5796 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 4
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction SCALA data reduction PHASER phasing