5SYM

Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FJ2APT1-CHAINA, PDB:1FJ2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1M sodium citrate, 22-24% PEG 3350, 200 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.67α = 90
b = 73.69β = 90
c = 81.82γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.9792APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.5543.511000.0570.0630.0220.99918.58.16353318.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.571000.4490.4810.1710.9137.83133

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAPT1-CHAINA, PDB:1FJ21.5543.516353331671000.180.1790.199RANDOM19.12
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]
-1.99181.03250.9593
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.75
t_other_torsion2.52
t_angle_deg1.09
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.75
t_other_torsion2.52
t_angle_deg1.09
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3350
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms108

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
BUSTERrefinement