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Crystal structure of the C-terminal domain of mouse acyl-CoA thioesterase 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPM PDB ENTRY 1VPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 20-30%PEG 3350, 0.1M Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.743 α = 90 b = 136.743 β = 90 c = 99.833 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.5 28.4 0.051 18.3 2.3 11896
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 2.5 2.57 0.52 2.1 2.3 1480
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 1VPM 2.5 28.39 11896 629 99.86 0.22516 0.22209 0.2184 0.2878 0.283 RANDOM 38.2
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] 0.42 0.21 0.42 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.36 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 19.979 r_dihedral_angle_1_deg 6.857 r_scangle_it 1.662 r_angle_refined_deg 1.375 r_scbond_it 1.02 r_mcangle_it 0.635 r_mcbond_it 0.377 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.36 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 19.979 r_dihedral_angle_1_deg 6.857 r_scangle_it 1.662 r_angle_refined_deg 1.375 r_scbond_it 1.02 r_mcangle_it 0.635 r_mcbond_it 0.377 r_nbtor_refined 0.3 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2187 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing