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Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with 4-O-methyl glucuronic acid
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 0.1M MGCL2 0.1M TRIS HCL PH6.5, 30% PEG 4K, 5% ISOPROPANOL, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.148 α = 90 b = 68.117 β = 90 c = 105.086 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 1.55 35 95 0.057 30.22 5.53 45059
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 1.55 1.61 71 0.358 3.39 2.25
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 1.55 14.82 45059 2401 95.5 0.16 0.158 0.1593 0.199 0.2009 RANDOM 12.7
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] -0.12 0.16 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.854 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 12.687 r_dihedral_angle_1_deg 6.1 r_scangle_it 3.266 r_scbond_it 2.034 r_angle_refined_deg 1.333 r_mcangle_it 1.246 r_mcbond_it 0.77 r_nbd_refined 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.854 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 12.687 r_dihedral_angle_1_deg 6.1 r_scangle_it 3.266 r_scbond_it 2.034 r_angle_refined_deg 1.333 r_mcangle_it 1.246 r_mcbond_it 0.77 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_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 2794 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling