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Crystal Structure of Apo-Hexameric Acyl-CoA Thioesterase
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 7.4 290 22 % PEG 3350, 0.13-0.17 M sodium formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.179 α = 90 b = 78.544 β = 90 c = 187.378 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 IMAGE PLATE RIGAKU 2007-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 25 23985
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1VPM 2.9 24.57 22694 22694 1210 99.66 0.28671 0.23405 0.23125 0.28671 0.308 RANDOM 64.587
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] -0.02 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 14.763 r_dihedral_angle_1_deg 5.075 r_angle_refined_deg 1.03 r_scangle_it 0.903 r_scbond_it 0.508 r_mcangle_it 0.466 r_nbtor_refined 0.289 r_mcbond_it 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 14.763 r_dihedral_angle_1_deg 5.075 r_angle_refined_deg 1.03 r_scangle_it 0.903 r_scbond_it 0.508 r_mcangle_it 0.466 r_nbtor_refined 0.289 r_mcbond_it 0.261 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 7215 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement d*TREK data reduction d*TREK data scaling