☰ Navigation Tabs
The native structure of the family 46 carbohydrate-binding module (CBM46) of 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 4UZ8 PDB ENTRY 4UZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.4-0.75 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE PROTEIN WAS COCRYSTALLISED WITH 10 MM OF 1,4-BETA-D-CELLOHEXAOSEIN 50 MM HEPES HCL PH 7.5, 200 MM NACL, 5 MM CACL2. 30%, V/V GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.19 α = 90 b = 121.19 β = 90 c = 77.28 γ = 90
Symmetry Space Group I 41 2 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 2012-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.46 44.37 99.8 0.13 9.7 8.2 10730
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 2.46 2.56 100 1.5 1.3 7.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4UZ8 2.46 85.69 10178 519 99.43 0.21558 0.21429 0.23997 0.2228 RANDOM 68.816
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] -4.99 -4.99 9.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 17.132 r_dihedral_angle_3_deg 15.114 r_dihedral_angle_1_deg 7.217 r_mcangle_it 2.156 r_scbond_it 1.42 r_angle_refined_deg 1.407 r_mcbond_it 1.321 r_mcbond_other 1.32 r_angle_other_deg 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_4_deg 17.132 r_dihedral_angle_3_deg 15.114 r_dihedral_angle_1_deg 7.217 r_mcangle_it 2.156 r_scbond_it 1.42 r_angle_refined_deg 1.407 r_mcbond_it 1.321 r_mcbond_other 1.32 r_angle_other_deg 0.844 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 1632 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction FAST_DP data scaling PHASER phasing