4X7O

Co-crystal Structure of PERK bound to 1-[5-(4-amino-2,7-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2,3-dihydro-1H-indol-1-yl]-2-[3-fluoro-5-(trifluoromethyl)phenyl]ethanone inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X7J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.15M NaCl, 0.1M MES pH 6.5, 12% PEG-3350
Crystal Properties
Matthews coefficientSolvent content
3.5965.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.366α = 90
b = 125.366β = 90
c = 58.203γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.99999ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.655099.70.0918.38.615481
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7497.50.67771467

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4X7J2.655077399.120.20.19870.2261RANDOM93.33
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]
-6.34-3.17-6.349.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.348
r_dihedral_angle_4_deg15.8
r_dihedral_angle_3_deg15.27
r_dihedral_angle_1_deg4.807
r_angle_refined_deg1.031
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2015
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms35

Software

Software
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing