4X7N | pdb_00004x7n

Co-crystal Structure of PERK bound to 4-[2-amino-4-methyl-3-(2-methylquinolin-6-yl)benzoyl]-1-methyl-2,5-diphenyl-1,2-dihydro-3H-pyrazol-3-one inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X7J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.4M Na/K Tartrate, 0.1M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.576	α = 90
b = 81.576	β = 90
c = 128.84	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2011-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.35	50	98.6	0.13	5.9	4.7		18581

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	92.7		0.604		3.8	1706

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4X7J	2.35	40.79	961	98.08	0.211	0.2092	0.21	0.2454	0.25	RANDOM	28.947

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]
0.29			0.29		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.949
r_dihedral_angle_4_deg	16.51
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_1_deg	4.667
r_scangle_it	1.575
r_angle_refined_deg	1.062
r_scbond_it	0.948
r_mcangle_it	0.638
r_mcbond_it	0.328
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.949
r_dihedral_angle_4_deg	16.51
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_1_deg	4.667
r_scangle_it	1.575
r_angle_refined_deg	1.062
r_scbond_it	0.948
r_mcangle_it	0.638
r_mcbond_it	0.328
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2122
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	50

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.