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Family 1 b-glucosidase from Thermotoga maritima
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 10MG/ML PROTEIN IN 15% PEG 4K, 0.2 M CAAC, 0.1M IMIDAZOLE PH7, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.91 α = 90 b = 94.98 β = 90 c = 113.928 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 2001-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.15 25 100 0.055 25.56 5.4 56583
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 2.15 2.23 100 0.331 5.14 5.4
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 2.15 72.55 53705 2878 99.6 0.204 0.201 0.1985 0.256 0.2515 RANDOM 40.28
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] -0.77 -0.25 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.667 r_scangle_it 4.158 r_scbond_it 2.724 r_mcangle_it 1.658 r_angle_other_deg 1.617 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.667 r_scangle_it 4.158 r_scbond_it 2.724 r_mcangle_it 1.658 r_angle_other_deg 1.617 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_refined_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 7108 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling