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Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with xylopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLX PDB ENTRY 1CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.2M MGCL2 0.1M TRIS HCL PH8, 30% PEG 4K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.158 α = 90 b = 67.901 β = 90 c = 104.794 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 IMAGE PLATE MARRESEARCH OSMICS 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.72 20 99.6 0.038 46 6.02 34539
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 1.72 1.78 98.7 0.174 10.35 5.49
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 1CLX 1.72 56.8 34539 1816 99.5 0.142 0.14 0.1523 0.186 0.1947 RANDOM 12.79
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] -0.01 0.24 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 17.228 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 6.294 r_scangle_it 3.617 r_scbond_it 2.5 r_angle_refined_deg 1.539 r_mcangle_it 1.347 r_mcbond_it 1.157 r_angle_other_deg 0.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 17.228 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 6.294 r_scangle_it 3.617 r_scbond_it 2.5 r_angle_refined_deg 1.539 r_mcangle_it 1.347 r_mcbond_it 1.157 r_angle_other_deg 0.865 r_mcbond_other 0.247 r_symmetry_vdw_other 0.238 r_nbd_refined 0.223 r_nbd_other 0.191 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.102 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined 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 2801 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing