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Beta-glucosidase from Thermotoga maritima in complex with deoxynojirimycin
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, PH 7, 0.2 M CALCIUM ACETATE. 25% ETHYLENE GLYCOL AS CRYO.
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.563 α = 90 b = 94.365 β = 90 c = 112.952 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 MARRESEARCH TOROIDAL MIRROR 2004-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.1 30 100 0.07 23.42 5.6 58779
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 2.1 2.18 100 0.37 4.7 5.6
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 2.1 72.55 55710 2970 99.7 0.199 0.196 0.1958 0.258 0.2578 RANDOM 32.69
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] 0.21 0.61 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 14.697 r_dihedral_angle_1_deg 6.195 r_scangle_it 2.495 r_scbond_it 1.706 r_angle_refined_deg 1.294 r_mcangle_it 1.157 r_mcbond_it 0.699 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 14.697 r_dihedral_angle_1_deg 6.195 r_scangle_it 2.495 r_scbond_it 1.706 r_angle_refined_deg 1.294 r_mcangle_it 1.157 r_mcbond_it 0.699 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.212 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 7143 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling