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Crystal structure of N-terminal mutant (V1L) 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 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M NaCl, 0.16M MgCl2, 0.05M Tris HCl pH 8.5, 18% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.88 α = 90 b = 76.58 β = 90 c = 176.73 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 MARMOSAIC 225 mm CCD MIRRORS 2012-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.82656 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.964 88.365 97.3 0.076 18.5 6.9 52548 52548
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 1.96 2.07 94.3 0.213 0.213 0.088 3.5 6.6 7277
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 1.964 40.19 52480 2682 97.1 0.1535 0.1516 0.1641 0.1901 0.1966 RANDOM 14.558
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] 0.38 -0.35 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 11.447 r_dihedral_angle_1_deg 6.152 r_angle_other_deg 1.986 r_angle_refined_deg 1.802 r_mcangle_it 1.404 r_mcbond_it 0.867 r_mcbond_other 0.867 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.734 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 11.447 r_dihedral_angle_1_deg 6.152 r_angle_other_deg 1.986 r_angle_refined_deg 1.802 r_mcangle_it 1.404 r_mcbond_it 0.867 r_mcbond_other 0.867 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_other 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5792 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 16
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing