3B7W

Crystal structure of human acyl-CoA synthetase medium-chain family member 2A, with L64P mutation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PG3PDB entry 1PG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M HEPES pH 7.5, 1.4M Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.7567.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.426α = 90
b = 109.173β = 90
c = 176.926γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCOSMIC MIRRORS2007-09-25MSINGLE 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
1250.5798.90.0770.0412.84.663810605802.06
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)
122.1198.20.8720.44624.7

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 1PG32506058060580322598.810.171360.169030.21385RANDOM28.86
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]
-1.850.81.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg16.409
r_dihedral_angle_3_deg13.089
r_scangle_it9.204
r_scbond_it7.72
r_dihedral_angle_1_deg6.089
r_mcangle_it4.599
r_mcbond_it3.823
r_angle_refined_deg1.446
r_mcbond_other1.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg16.409
r_dihedral_angle_3_deg13.089
r_scangle_it9.204
r_scbond_it7.72
r_dihedral_angle_1_deg6.089
r_mcangle_it4.599
r_mcbond_it3.823
r_angle_refined_deg1.446
r_mcbond_other1.159
r_angle_other_deg0.939
r_nbd_refined0.198
r_symmetry_vdw_other0.198
r_nbd_other0.195
r_nbtor_refined0.173
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.092
r_nbtor_other0.088
r_chiral_restr0.082
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms4126
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing