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Very high resolution structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AOS PDB ENTRY 5AOS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 20 MG/ML OF PROTEIN IN 0.2 M SODIUM ACETATE, 0.1 M CACODYLIC ACID PH 6.5, 30%(W/V) POLYETHYLENE GLYCOL 8000. 30%(V/V) GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 1.85 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.272 α = 90 b = 45.02 β = 90 c = 49.453 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 2014-11-15 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 1.02 33.29 99.6 0.05 16.2 6.2 42277
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 1.02 1.05 96.5 0.94 1.5 5.4
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 5AOS 1.02 33.29 47545 2472 99.64 0.16472 0.16443 0.1721 0.17028 0.178 RANDOM 14.359
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] 1.16 -0.43 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.36 r_sphericity_free 23.507 r_dihedral_angle_3_deg 11.738 r_sphericity_bonded 11.287 r_dihedral_angle_4_deg 10.626 r_dihedral_angle_1_deg 7.476 r_rigid_bond_restr 2.923 r_scbond_it 2.044 r_mcangle_it 1.66 r_angle_refined_deg 1.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.36 r_sphericity_free 23.507 r_dihedral_angle_3_deg 11.738 r_sphericity_bonded 11.287 r_dihedral_angle_4_deg 10.626 r_dihedral_angle_1_deg 7.476 r_rigid_bond_restr 2.923 r_scbond_it 2.044 r_mcangle_it 1.66 r_angle_refined_deg 1.613 r_mcbond_it 1.277 r_mcbond_other 1.234 r_angle_other_deg 0.757 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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_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 802 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing