☰ Navigation Tabs
X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GTN PDB ENTRY 3GTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M POTASSIUM SULFATE 20 % (W/V) POLYETHYLENE GLYCOL 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.09 α = 83.15 b = 47.463 β = 73.41 c = 53.62 γ = 65.87
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.4 42.93 97.2 0.2 3.5 4.6 76088 3.5
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 1.4 1.48 95.6 0.86 1.3 4.6
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 3GTN 1.4 51.39 72006 3804 96.85 0.14958 0.14841 0.1555 0.1715 0.1772 RANDOM
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] 0.54 -0.19 0.26 -0.16 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.752 r_dihedral_angle_4_deg 23.36 r_dihedral_angle_3_deg 12.118 r_dihedral_angle_1_deg 6.652 r_long_range_B_other 6.301 r_long_range_B_refined 6.298 r_scangle_other 2.697 r_mcangle_other 1.959 r_mcangle_it 1.954 r_angle_refined_deg 1.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.752 r_dihedral_angle_4_deg 23.36 r_dihedral_angle_3_deg 12.118 r_dihedral_angle_1_deg 6.652 r_long_range_B_other 6.301 r_long_range_B_refined 6.298 r_scangle_other 2.697 r_mcangle_other 1.959 r_mcangle_it 1.954 r_angle_refined_deg 1.837 r_scbond_it 1.752 r_scbond_other 1.749 r_mcbond_it 1.18 r_mcbond_other 1.105 r_angle_other_deg 0.943 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3168 Nucleic Acid Atoms Solvent Atoms 647 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing