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Structure of the wild-type cellobiohydrolase Cel6A from Humicolas insolens in complex with a fluorescent substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVW PDB ENTRY 2BVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 THE PROTEIN WAS CONCENTRATED IN WATER TO 7 MG/ML IT WAS INCUBATED 1H PRIOR CRYSTALLISATION WITH THE 5MM OF THE SUBSTRATE 16% PEG5KMME AND 200 MM CALCIUM ACETATE WERE USED AS PRECIPITANT AND 100 MM SODIUM ACETATE PH 4.6 AS BUFFER.
Crystal Properties Matthews coefficient Solvent content 2.1 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.763 α = 90 b = 155.681 β = 118.42 c = 51.218 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 CCD ADSC CCD 2000-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.75 40 97.5 0.041 17.3 2.2 69418 2
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 1.75 1.81 91.3 0.128 6 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 2BVW 1.75 38.92 63815 3394 97.7 0.135 0.133 0.1503 0.168 0.1827 RANDOM 9.06
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] 1.68 0.25 -1.26 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.904 r_scangle_it 3.5 r_scbond_it 2.331 r_angle_refined_deg 1.578 r_mcangle_it 1.348 r_angle_other_deg 0.911 r_mcbond_it 0.796 r_symmetry_vdw_other 0.258 r_nbd_other 0.255 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.904 r_scangle_it 3.5 r_scbond_it 2.331 r_angle_refined_deg 1.578 r_mcangle_it 1.348 r_angle_other_deg 0.911 r_mcbond_it 0.796 r_symmetry_vdw_other 0.258 r_nbd_other 0.255 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.1 r_nbtor_other 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5630 Nucleic Acid Atoms Solvent Atoms 715 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing