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Beta-glucosidase from Thermotoga maritima in complex with cyclophellitol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OD0 PDB ENTRY 1OD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10 MG/ML PROTEIN. 15% PEG 4K, 0.1 M IMIDAZOLE, 0.2 M CALCIUM ACETATE., pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.699 α = 90 b = 94.466 β = 90 c = 113.591 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 CCD ADSC CCD SILICON TOROIDAL MIRROR COATED WITH RHODIUM 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.9 30 94.6 0.04 19.2 3.3 76161
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 1.9 1.97 78.3 0.28 3.5 2.4
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 1OD0 1.9 72.74 72208 3815 94.3 0.198 0.196 0.1926 0.244 0.2371 RANDOM 35.74
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] -0.58 0.23 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.925 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_1_deg 6.133 r_scangle_it 3.027 r_scbond_it 2.068 r_angle_refined_deg 1.439 r_mcangle_it 1.404 r_mcbond_it 0.889 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.925 r_dihedral_angle_4_deg 18.314 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_1_deg 6.133 r_scangle_it 3.027 r_scbond_it 2.068 r_angle_refined_deg 1.439 r_mcangle_it 1.404 r_mcbond_it 0.889 r_nbtor_refined 0.314 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 7118 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling