3DAY

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C5EPDB entry 3C5E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529325% PEG 3350, 0.20M NaCl, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.508α = 90
b = 97.835β = 90
c = 120.415γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCOSMIC2008-03-17MSINGLE 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
11.9532.7298.20.0890.055113.548550459632
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)
11.952.0693.40.4910.3032.33.36604

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3C5E1.9531.514596345963244197.880.163980.163980.160950.22033RANDOM13.974
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]
-0.26-0.550.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.695
r_dihedral_angle_4_deg17.191
r_dihedral_angle_3_deg13.532
r_scangle_it8.845
r_scbond_it6.747
r_dihedral_angle_1_deg6.312
r_mcangle_it4.216
r_mcbond_it3.048
r_angle_refined_deg1.555
r_mcbond_other1.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.695
r_dihedral_angle_4_deg17.191
r_dihedral_angle_3_deg13.532
r_scangle_it8.845
r_scbond_it6.747
r_dihedral_angle_1_deg6.312
r_mcangle_it4.216
r_mcbond_it3.048
r_angle_refined_deg1.555
r_mcbond_other1.031
r_angle_other_deg0.989
r_chiral_restr0.094
r_bond_refined_d0.017
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 Atoms4150
Nucleic Acid Atoms
Solvent Atoms763
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing