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Structural studies of a thermophilic esterase from Thermogutta terrifontis (L37A mutant with butyrate bound)
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 2.04 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.23 α = 90 b = 43.23 β = 90 c = 227.83 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.08 37.97 100 0.07 14.8 9.3 107910 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 1.08 1.11 99.9 1.12 2 8.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XUA 1.08 37.97 102497 5279 99.96 0.11459 0.11351 0.13 0.13561 0.1485 RANDOM 16.721
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] -0.07 -0.04 -0.07 0.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.334 r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 16.274 r_dihedral_angle_3_deg 14.797 r_sphericity_bonded 14.058 r_dihedral_angle_1_deg 6.247 r_scbond_it 5.932 r_mcangle_it 3.811 r_mcbond_it 2.989 r_mcbond_other 2.955
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.334 r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 16.274 r_dihedral_angle_3_deg 14.797 r_sphericity_bonded 14.058 r_dihedral_angle_1_deg 6.247 r_scbond_it 5.932 r_mcangle_it 3.811 r_mcbond_it 2.989 r_mcbond_other 2.955 r_rigid_bond_restr 1.944 r_angle_refined_deg 1.806 r_angle_other_deg 1.056 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2139 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOLREP phasing