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X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.25 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CKQ PDB ENTRY 4CKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25 % (V/V) PEG 3350, 0.2 M CACL2, 0.1 M HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.64 α = 83.37 b = 46.74 β = 73.53 c = 53.07 γ = 65.79
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 KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL 2014-03-13 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 1.25 50.9 89.8 0.07 15.21 4 96003 1.58
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 1.25 1.29 75.8 0.83 1.58 3.7
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 4CKQ 1.25 42.63 94054 1949 89.7 0.133 0.133 0.1423 0.166 0.1731 RANDOM 11.003
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 0.25 -0.21 -0.13 0.66 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.363 r_sphericity_free 26.461 r_dihedral_angle_4_deg 23.825 r_dihedral_angle_3_deg 10.848 r_sphericity_bonded 6.961 r_dihedral_angle_1_deg 6.499 r_rigid_bond_restr 2.465 r_angle_refined_deg 1.395 r_angle_other_deg 0.79 r_mcbond_it 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.363 r_sphericity_free 26.461 r_dihedral_angle_4_deg 23.825 r_dihedral_angle_3_deg 10.848 r_sphericity_bonded 6.961 r_dihedral_angle_1_deg 6.499 r_rigid_bond_restr 2.465 r_angle_refined_deg 1.395 r_angle_other_deg 0.79 r_mcbond_it 0.72 r_mcbond_other 0.713 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing