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Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with arabinofuranose alpha-1,3 linked to xylobiose
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 6.5 0.35M MGCL2 0.1M TRIS HCL PH6.5, 30% PEG 4K, 5% PEG 400, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.014 α = 90 b = 67.7 β = 90 c = 105.124 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 TOROIDAL MIRROR 2003-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.43 35 83.3 0.055 26.02 5.62 49417
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 1.43 1.48 20.5 0.334 1.94 1.38
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UQY 1.43 33.9 49417 2593 83.4 0.153 0.151 0.186 0.2102 RANDOM 10.72
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] -0.1 0.11 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.622 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_4_deg 14.711 r_dihedral_angle_1_deg 6.129 r_scangle_it 3.49 r_scbond_it 2.279 r_angle_other_deg 2.051 r_angle_refined_deg 1.609 r_mcangle_it 1.58 r_mcbond_it 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.622 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_4_deg 14.711 r_dihedral_angle_1_deg 6.129 r_scangle_it 3.49 r_scbond_it 2.279 r_angle_other_deg 2.051 r_angle_refined_deg 1.609 r_mcangle_it 1.58 r_mcbond_it 1.041 r_symmetry_vdw_other 0.289 r_mcbond_other 0.254 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.246 r_nbd_other 0.213 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.169 r_nbtor_other 0.121 r_chiral_restr 0.098 r_metal_ion_refined 0.066 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2792 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling