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Crystal structure of Bacillus subtilis family-11 xylanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XNB PDB ENTRY 1XNB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.445 α = 90 b = 186.209 β = 90 c = 37.979 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 4 Mirror 2002-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 20 97.6 0.044 0.044 13.7 3.7 178663 1 1 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.48 87.3 0.301 0.301 2.5 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1XNB 1.4 20 1 178662 169733 8929 97.5 0.19828 0.19828 0.1973 0.2051 0.21733 0.2041 RANDOM 15.159
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] -0.08 0.13 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.009 r_scangle_it 3.036 r_scbond_it 2.291 r_angle_refined_deg 1.701 r_mcangle_it 1.536 r_mcbond_it 0.937 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.201 r_chiral_restr 0.114 r_xyhbond_nbd_refined 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.009 r_scangle_it 3.036 r_scbond_it 2.291 r_angle_refined_deg 1.701 r_mcangle_it 1.536 r_mcbond_it 0.937 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.201 r_chiral_restr 0.114 r_xyhbond_nbd_refined 0.101 r_symmetry_hbond_refined 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7275 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing