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Structural studies of a thermophilic esterase from Thermogutta terrifontis (cacodylate complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XUA PDB ENTRY 2XUA
Crystallization Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.31 α = 90 b = 43.31 β = 90 c = 226.85 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PIXEL M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.06 37.81 99.7 0.06 18.5 8.9 113560 2
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 1.06 1.09 96.2 0.63 2.1 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XUA 1.06 37.81 107919 5507 99.65 0.10393 0.10295 0.12312 0.133 RANDOM 14.171
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 0.02 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 31.17 r_dihedral_angle_2_deg 30.514 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 12.491 r_sphericity_bonded 11.042 r_dihedral_angle_1_deg 5.927 r_scbond_it 3.958 r_rigid_bond_restr 2.785 r_mcangle_it 2.223 r_mcbond_it 1.705
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 31.17 r_dihedral_angle_2_deg 30.514 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_3_deg 12.491 r_sphericity_bonded 11.042 r_dihedral_angle_1_deg 5.927 r_scbond_it 3.958 r_rigid_bond_restr 2.785 r_mcangle_it 2.223 r_mcbond_it 1.705 r_angle_refined_deg 1.699 r_mcbond_other 1.651 r_angle_other_deg 0.904 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2104 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOLREP phasing