3EQ6

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M Mg(form), 15% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.028α = 90
b = 98.041β = 94.12
c = 116.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCOSMIC2008-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
12.424.9999.30.1070.0783.3498664730022
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)
12.42.53980.4940.3232.23.17167

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 3B7W2.421.734986647300253199.410.189280.186740.23638RANDOM17.19
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]
0.71-1.79-1.50.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.233
r_dihedral_angle_3_deg15.624
r_dihedral_angle_4_deg13.503
r_scangle_it8.481
r_scbond_it6.625
r_dihedral_angle_1_deg6.213
r_mcangle_it3.849
r_mcbond_it2.335
r_angle_refined_deg1.576
r_angle_other_deg0.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.233
r_dihedral_angle_3_deg15.624
r_dihedral_angle_4_deg13.503
r_scangle_it8.481
r_scbond_it6.625
r_dihedral_angle_1_deg6.213
r_mcangle_it3.849
r_mcbond_it2.335
r_angle_refined_deg1.576
r_angle_other_deg0.944
r_mcbond_other0.398
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms8225
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms152

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling