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X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.28 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, 0.1 M HEPES 7.5, 0.2 M CACL2
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.94 α = 68.11 b = 46.07 β = 80.19 c = 59.05 γ = 60.99
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 1.28 40.18 95.1 0.06 23 4.3 96062 1.5
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 1.28 1.3 90.1 0.2 10.7 4
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 1.28 40.18 93795 2006 94.79 0.095 0.094 0.1119 0.111 0.1275 RANDOM 9.857
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] 0.22 0.01 -0.1 -0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.934 r_sphericity_free 23.934 r_dihedral_angle_4_deg 22.278 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 6.623 r_sphericity_bonded 6.162 r_rigid_bond_restr 2.015 r_angle_refined_deg 1.504 r_angle_other_deg 0.831 r_mcbond_it 0.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.934 r_sphericity_free 23.934 r_dihedral_angle_4_deg 22.278 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 6.623 r_sphericity_bonded 6.162 r_rigid_bond_restr 2.015 r_angle_refined_deg 1.504 r_angle_other_deg 0.831 r_mcbond_it 0.675 r_mcbond_other 0.673 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 601 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing