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High resolution structure of the full length tri-modular endo-beta-1, 4-glucanase B (Cel5B) from Bacillus halodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDZ PDB ENTRY 3NDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M CALCIUM ACETATE, 0.1 M CACODYLATE PH 6.5, 8% PEG 8K WITH 30% GLYCEROL ADDED TO ABOVE AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.22 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.22 α = 90 b = 141.84 β = 90 c = 50.82 γ = 90
Symmetry Space Group P 21 21 2
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 2013-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.64 51.27 99.9 0.07 19.7 7.2 66600
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 1.64 1.68 99.8 0.74 2.6 6.8
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 3NDZ 1.64 51.27 63160 3376 99.89 0.15562 0.1543 0.1667 0.18094 0.1897 RANDOM 19.389
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] -0.7 0.22 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.041 r_dihedral_angle_4_deg 16.311 r_dihedral_angle_3_deg 11.23 r_dihedral_angle_1_deg 5.804 r_scbond_it 1.93 r_mcangle_it 1.846 r_mcbond_it 1.135 r_mcbond_other 1.119 r_angle_refined_deg 1.066 r_angle_other_deg 0.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.041 r_dihedral_angle_4_deg 16.311 r_dihedral_angle_3_deg 11.23 r_dihedral_angle_1_deg 5.804 r_scbond_it 1.93 r_mcangle_it 1.846 r_mcbond_it 1.135 r_mcbond_other 1.119 r_angle_refined_deg 1.066 r_angle_other_deg 0.704 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4334 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling BALBES phasing