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Crystal structure of a glycoside hydrolase family 11 xylanase from Bacillus subtilis in complex with xylotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BCX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.2M ammonium sulphate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.638 α = 90 b = 78.98 β = 101.49 c = 54.4 γ = 90
Symmetry Space Group P 1 21 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 CCD MAR CCD 165 mm 2006-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9762 EMBL/DESY, HAMBURG BW7A
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 1.8 20 99.4 0.044 23.3 31423 30942 2 1.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.83 99.9 0.089 11.5 1547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1BCX 1.8 19.91 27803 27803 3117 99.27 0.15038 0.14624 0.1456 0.18807 0.1866 RANDOM 14.35
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] 0.05 -0.31 0.05 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_4_deg 11.245 r_dihedral_angle_1_deg 9.44 r_scangle_it 2.639 r_scbond_it 1.79 r_angle_refined_deg 1.346 r_mcangle_it 1.247 r_mcbond_it 0.701 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.527 r_dihedral_angle_3_deg 11.614 r_dihedral_angle_4_deg 11.245 r_dihedral_angle_1_deg 9.44 r_scangle_it 2.639 r_scbond_it 1.79 r_angle_refined_deg 1.346 r_mcangle_it 1.247 r_mcbond_it 0.701 r_nbtor_refined 0.312 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2910 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing