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Family 1 b-glucosidase from Thermotoga maritima in complex with tetrahydrooxazine
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 4000, 0.2 M CAAC, 0.1 M IMIDAZOLE PH7, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.562 α = 90 b = 94.595 β = 90 c = 113.48 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 2003-04-15 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 2 40 95.7 0.061 21.6 5.22 66518
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 2.07 100 0.457 3.12 5.5
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 2 72.55 63027 3277 95.6 0.207 0.204 0.203 0.258 0.2561 RANDOM 34
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] -0.04 -0.49 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 16.535 r_dihedral_angle_1_deg 6.126 r_scangle_it 2.926 r_scbond_it 1.989 r_angle_refined_deg 1.415 r_mcangle_it 1.345 r_mcbond_it 0.796 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 16.535 r_dihedral_angle_1_deg 6.126 r_scangle_it 2.926 r_scbond_it 1.989 r_angle_refined_deg 1.415 r_mcangle_it 1.345 r_mcbond_it 0.796 r_nbtor_refined 0.315 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.107 r_bond_refined_d 0.014 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 7196 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling