5OQ5 | pdb_00005oq5

Structure of CHK1 8-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.4	α = 90
b = 66.57	β = 101.58
c = 55.08	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2016-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.38	33.28	96.4	0.027	0.033	0.019	0.998	18	2.7		63516

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)	Redundancy	Number Unique Reflections (All)
1	1.38	1.42	89.4		0.787	1.009	0.624	0.612		2.1

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	5OOT	1.4	20	58098	3013	96.64	0.1695	0.1687	0.17	0.1852	0.19	RANDOM	32.723

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]
-1.45		-0.49	0.11		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.495
r_dihedral_angle_4_deg	21.177
r_dihedral_angle_3_deg	15.434
r_dihedral_angle_1_deg	5.61
r_angle_refined_deg	2.554
r_angle_other_deg	1.19
r_chiral_restr	0.15
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.495
r_dihedral_angle_4_deg	21.177
r_dihedral_angle_3_deg	15.434
r_dihedral_angle_1_deg	5.61
r_angle_refined_deg	2.554
r_angle_other_deg	1.19
r_chiral_restr	0.15
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2106
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction

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.