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Crystal Structure of a GH8 xylanase from Teredinibacter turnerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291.2 sodium acetate (0.1M, pH 5.0), NaCl (0.2 M), polyethylene glycol 6000 16%.
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.54 α = 90 b = 72.995 β = 90 c = 90.866 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 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 51 99.4 9.6 4.3 80610
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42
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 1WU4 1.4 56.97 76616 3924 99.17 0.15369 0.15279 0.1627 0.17142 0.1762 RANDOM 14.305
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] 0.94 0.54 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 11.894 r_dihedral_angle_1_deg 5.632 r_long_range_B_refined 3.837 r_long_range_B_other 3.837 r_scangle_other 2.917 r_scbond_it 1.919 r_scbond_other 1.919 r_angle_refined_deg 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 11.894 r_dihedral_angle_1_deg 5.632 r_long_range_B_refined 3.837 r_long_range_B_other 3.837 r_scangle_other 2.917 r_scbond_it 1.919 r_scbond_other 1.919 r_angle_refined_deg 1.683 r_mcangle_other 1.569 r_mcangle_it 1.567 r_mcbond_it 1.06 r_mcbond_other 1.053 r_angle_other_deg 1.051 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing