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Beta-glucosidase from Thermotoga maritima in complex with phenethyl- substituted glucoimidazole
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 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 = 94.365 α = 90 b = 94.52 β = 90 c = 113.582 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 SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2002-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.97 30 97.6 0.05 21.93 4.8 70563
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 1.97 2.04 97.9 0.39 2.83 3.5
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 1.97 29.88 66767 3537 97.2 0.195 0.192 0.1927 0.244 0.2448 RANDOM 32.31
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] -0.66 -0.2 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.153 r_scangle_it 2.718 r_scbond_it 1.86 r_angle_refined_deg 1.374 r_mcangle_it 1.265 r_mcbond_it 0.802 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.153 r_scangle_it 2.718 r_scbond_it 1.86 r_angle_refined_deg 1.374 r_mcangle_it 1.265 r_mcbond_it 0.802 r_nbtor_refined 0.317 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.094 r_bond_refined_d 0.013 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 7146 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling