3C5E

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.529317% PEG 10000, 0.1M Ammonium acetate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.7α = 90
b = 98.073β = 90
c = 120.263γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2007-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.651.399.50.0710.04311.63.6841812
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)
11.61.69970.5940.37223.3

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 3B7W1.6498418184181450099.460.158060.156110.19423RANDOM17.104
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]
-0.02-1.051.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.165
r_dihedral_angle_4_deg13.49
r_dihedral_angle_3_deg12.372
r_scangle_it7.869
r_dihedral_angle_1_deg6.635
r_scbond_it5.586
r_mcangle_it3.843
r_mcbond_it2.571
r_angle_refined_deg1.653
r_angle_other_deg0.979
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.165
r_dihedral_angle_4_deg13.49
r_dihedral_angle_3_deg12.372
r_scangle_it7.869
r_dihedral_angle_1_deg6.635
r_scbond_it5.586
r_mcangle_it3.843
r_mcbond_it2.571
r_angle_refined_deg1.653
r_angle_other_deg0.979
r_mcbond_other0.791
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms4149
Nucleic Acid Atoms
Solvent Atoms776
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing