3GPC

Crystal structure of human Acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a complex with CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B7WPDB ENTRY 3B7W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529325% PEG3350, 0.20M (NH4)2SO4, 0.1M BIS-TRIS, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.604α = 90
b = 97.535β = 89.99
c = 118.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2008-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.5418SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95077.90.0740.0538.32.4771197327922
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)RedundancyNumber Unique Reflections (All)
11.9281.70.3550.2652.52.311811

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3B7W1.9507711973279381277.630.165470.162360.2255RANDOM16.683
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]
-0.38-0.17-0.891.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.841
r_dihedral_angle_3_deg15.257
r_dihedral_angle_4_deg13.776
r_scangle_it8.779
r_dihedral_angle_1_deg6.787
r_scbond_it6.416
r_mcangle_it3.981
r_mcbond_it2.706
r_angle_refined_deg1.611
r_angle_other_deg0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.841
r_dihedral_angle_3_deg15.257
r_dihedral_angle_4_deg13.776
r_scangle_it8.779
r_dihedral_angle_1_deg6.787
r_scbond_it6.416
r_mcangle_it3.981
r_mcbond_it2.706
r_angle_refined_deg1.611
r_angle_other_deg0.91
r_mcbond_other0.827
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms8200
Nucleic Acid Atoms
Solvent Atoms784
Heterogen Atoms83

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling