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Crystal structure of alkaline thermophlic xylanase from Bacillus sp. (NCL 86-6-10) with complex xylotriose: Xylotriose cleaved to xylobiose and xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 40% Isopropanol, 0.4M Sodium citrate, 0.1M Sodium cacodylate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.363 α = 90 b = 78.363 β = 90 c = 140.84 γ = 90
Symmetry Space Group P 43 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 295 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.4 68.52 99.8 0.052 0.045 32.11 17873 17.561
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) 2.4 30 99.8 0.052 0.045 32.11 190598
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 1H4G 2.4 68.5 16919 912 99.77 0.19443 0.19185 0.1871 0.2428 0.2309 RANDOM 17.598
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] -0.74 -0.74 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.39 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 7.098 r_scangle_it 2.05 r_scbond_it 1.414 r_angle_refined_deg 1.38 r_mcangle_it 0.984 r_mcbond_it 0.557 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.39 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 7.098 r_scangle_it 2.05 r_scbond_it 1.414 r_angle_refined_deg 1.38 r_mcangle_it 0.984 r_mcbond_it 0.557 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction HKL-2000 data scaling AMoRE phasing