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Crystal structure of human Acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a complex with CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7W PDB ENTRY 3B7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 25% PEG3350, 0.20M (NH4)2SO4, 0.1M BIS-TRIS, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.604 α = 90 b = 97.535 β = 89.99 c = 118.21 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 325 mm CCD 2008-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.5418 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 77.9 0.074 0.053 8.3 2.4 77119 73279 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 81.7 0.355 0.265 2.5 2.3 11811
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 (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 3B7W 1.9 50 77119 73279 3812 77.63 0.16547 0.16236 0.1687 0.2255 0.2313 RANDOM 16.683
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] -0.38 -0.17 -0.89 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_4_deg 13.776 r_scangle_it 8.779 r_dihedral_angle_1_deg 6.787 r_scbond_it 6.416 r_mcangle_it 3.981 r_mcbond_it 2.706 r_angle_refined_deg 1.611 r_angle_other_deg 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.841 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_4_deg 13.776 r_scangle_it 8.779 r_dihedral_angle_1_deg 6.787 r_scbond_it 6.416 r_mcangle_it 3.981 r_mcbond_it 2.706 r_angle_refined_deg 1.611 r_angle_other_deg 0.91 r_mcbond_other 0.827 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8200 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 83
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling