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Crystal structure of human 3-oxoacid CoA transferase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M3E PDB entry 1M3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 25% PEG 3350, 0.2 M NaCl, 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.956 α = 90 b = 168.492 β = 105.86 c = 95.322 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD 2008-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9786 SLS X10SA
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 2.2 48.11 98.6 0.083 7.4 2.3 92253 92253 30
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 2.32 97 0.526 1.9 2.1 13203
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1M3E 2.2 48.11 90754 90754 1302 98.41 0.17887 0.17887 0.17821 0.181 0.22473 0.2267 RANDOM 29.557
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] 0.11 -1.34 0.48 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.75 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_1_deg 6.987 r_scangle_it 2.898 r_scbond_it 1.93 r_angle_refined_deg 1.556 r_mcangle_it 1.099 r_angle_other_deg 0.966 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.75 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_1_deg 6.987 r_scangle_it 2.898 r_scbond_it 1.93 r_angle_refined_deg 1.556 r_mcangle_it 1.099 r_angle_other_deg 0.966 r_mcbond_it 0.711 r_symmetry_vdw_refined 0.263 r_nbd_other 0.197 r_nbd_refined 0.191 r_symmetry_vdw_other 0.185 r_nbtor_refined 0.172 r_mcbond_other 0.168 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.09 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13833 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing