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Crystal structure of aromatic mutant (Y343A) 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, 150mM MgCl2, 0.1M Tris-HCl pH 8.5, 15% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.86 α = 90 b = 80.11 β = 111.19 c = 69.21 γ = 90
Symmetry Space Group C 1 2 1
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 2010-09-03 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 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 2.3 64.531 91.9 0.059 0.069 0.034 14.3 3.8 15361 15361
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 2.3 2.42 93.8 0.218 0.218 0.13 3.5 3.6 2271
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 2.3 64.53 14620 732 91.42 0.1807 0.178 0.1841 0.2349 0.2402 RANDOM 32.416
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] -1.66 -0.91 1.28 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_3_deg 13.452 r_dihedral_angle_4_deg 13.302 r_dihedral_angle_1_deg 5.899 r_mcangle_it 1.297 r_angle_refined_deg 1.095 r_angle_other_deg 0.753 r_mcbond_other 0.747 r_mcbond_it 0.746 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_3_deg 13.452 r_dihedral_angle_4_deg 13.302 r_dihedral_angle_1_deg 5.899 r_mcangle_it 1.297 r_angle_refined_deg 1.095 r_angle_other_deg 0.753 r_mcbond_other 0.747 r_mcbond_it 0.746 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2888 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction SCALA data reduction PHASER phasing