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The ultra high resolution structure of a novel alpha-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405 with bound trimethyl N-Oxide (TRS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C7E PDB ENTRY 3C7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M TRIS PH 8.5, 20% PEG 2000 MONOMETHYL ETHER, 0.2 M TRIMETHYL N-OXIDE, WITH PARATONE-N USED AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.44 α = 90 b = 67.7 β = 113.09 c = 51.01 γ = 90
Symmetry Space Group P 1 21 1
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 2013-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 0.97 67.76 71.5 0.08 16.5 7.2 119795
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 0.97 1 6.7 0.52 2 4.2
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 3C7E 0.97 39.95 113299 5972 71.32 0.10413 0.1031 0.1176 0.12384 0.1367 RANDOM 11.11
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] -0.3 -0.16 -0.27 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_sphericity_free 21.023 r_dihedral_angle_4_deg 14.781 r_dihedral_angle_3_deg 11.095 r_dihedral_angle_1_deg 6.811 r_sphericity_bonded 6.373 r_rigid_bond_restr 3.873 r_angle_refined_deg 1.799 r_scbond_it 1.271 r_mcangle_it 1.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_sphericity_free 21.023 r_dihedral_angle_4_deg 14.781 r_dihedral_angle_3_deg 11.095 r_dihedral_angle_1_deg 6.811 r_sphericity_bonded 6.373 r_rigid_bond_restr 3.873 r_angle_refined_deg 1.799 r_scbond_it 1.271 r_mcangle_it 1.257 r_angle_other_deg 1.06 r_mcbond_it 0.891 r_mcbond_other 0.858 r_chiral_restr 0.125 r_bond_refined_d 0.017 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_mcangle_other 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 2365 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling BALBES phasing