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Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with arabinofuranose alpha 1,3 linked to xylotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UQY PDB ENTRY 1UQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2M MGCL2 0.1M TRIS HCL PH8.5, 30% PEG 4K, 5% PEG 400., pH 8.50
Crystal Properties Matthews coefficient Solvent content 2 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.924 α = 90 b = 67.659 β = 90 c = 104.782 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 120 CCD ADSC CCD VERTICAL FOCUSING MIRROR 2003-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 30 98.3 0.076 1.93 3.25 42050
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 90.3 0.432 1.93 2.23
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 PDB ENTRY 1UQY 1.6 19.28 42034 2209 98.8 0.154 0.152 0.1655 0.189 0.1999 RANDOM 11.84
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] 0.29 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_1_deg 6.128 r_scangle_it 2.67 r_scbond_it 1.849 r_angle_refined_deg 1.319 r_angle_other_deg 1.244 r_mcangle_it 1.026 r_mcbond_it 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_4_deg 16.235 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_1_deg 6.128 r_scangle_it 2.67 r_scbond_it 1.849 r_angle_refined_deg 1.319 r_angle_other_deg 1.244 r_mcangle_it 1.026 r_mcbond_it 0.896 r_symmetry_vdw_other 0.25 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.213 r_nbd_other 0.19 r_mcbond_other 0.179 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.143 r_nbtor_other 0.095 r_chiral_restr 0.083 r_metal_ion_refined 0.02 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2838 Nucleic Acid Atoms Solvent Atoms 591 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling