4G34 | pdb_00004g34

Crystal Structure of GSK6924 Bound to PERK (R587-R1092, delete A660-T867) at 2.70 A Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A19	PDB ENTRY 2A19

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	100 mM BTP, pH 7.0, 3.5 - 4.9 M linear gradient of ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.46	α = 90
b = 101.46	β = 90
c = 158.312	γ = 120

Symmetry
Space Group	P 61 2 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	CCD	RAYONIX MX-300		2010-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G

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	2.7	45.239	100	0.092	32.5	20.8	13940	13061			39

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	2.7	2.8	100		0.584	5.67	19.4	1354

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	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	PDB ENTRY 2A19	2.7	45.239	13061	688	99.28	0.21049	0.20818	0.21	0.25762	0.25	RANDOM	66.856

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]
1.76	0.88		1.76		-2.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.345
r_dihedral_angle_4_deg	16.892
r_dihedral_angle_3_deg	16.074
r_dihedral_angle_1_deg	4.683
r_scangle_it	1.664
r_angle_refined_deg	1.125
r_scbond_it	0.956
r_mcangle_it	0.626
r_mcbond_it	0.318
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.345
r_dihedral_angle_4_deg	16.892
r_dihedral_angle_3_deg	16.074
r_dihedral_angle_1_deg	4.683
r_scangle_it	1.664
r_angle_refined_deg	1.125
r_scbond_it	0.956
r_mcangle_it	0.626
r_mcbond_it	0.318
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1997
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MD2	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.