☰ Navigation Tabs
Biochemical and structural characterisation of an alkaline family GH5 cellulase from a shipworm symbiont
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M MgCl2,
0.1 M Tris-HCl, pH 8.5
25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 35.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.041 α = 90 b = 68.426 β = 90 c = 87.188 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 2016-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91842 BESSY 14.1
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 45.04 98 0.077 11.5 6.6 143241 6.32
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 1.02 77.7 0.609 1.5 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1 53.83 140934 2221 97.85 0.11275 0.11242 0.1123 0.13342 0.1324 RANDOM 10.485
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] -0.12 0.08 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.53 r_sphericity_free 21.888 r_dihedral_angle_3_deg 12.133 r_dihedral_angle_4_deg 11.248 r_sphericity_bonded 7.478 r_dihedral_angle_1_deg 7.052 r_rigid_bond_restr 6.912 r_long_range_B_refined 2.888 r_long_range_B_other 2.616 r_scangle_other 2.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.53 r_sphericity_free 21.888 r_dihedral_angle_3_deg 12.133 r_dihedral_angle_4_deg 11.248 r_sphericity_bonded 7.478 r_dihedral_angle_1_deg 7.052 r_rigid_bond_restr 6.912 r_long_range_B_refined 2.888 r_long_range_B_other 2.616 r_scangle_other 2.424 r_scbond_it 2.371 r_scbond_other 2.331 r_angle_refined_deg 2.256 r_mcangle_other 1.36 r_mcangle_it 1.353 r_mcbond_it 1.237 r_mcbond_other 1.2 r_angle_other_deg 1.142 r_chiral_restr 0.143 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2325 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing