5FD2

B-Raf wild-type kinase domain in complex with a purinylpyridinylamino-based inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 8000, tacsimate, tris

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.79	α = 90
b = 80.088	β = 90
c = 245.253	γ = 90

Symmetry
Space Group	C 2 2 21

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		2010-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.88	50	99.9	0.101	0.11	0.044	8.9	6.3		16728		-3	79.3

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	2.88	2.98	100		0.727	0.794	0.316	0.755	2.6	6.2	1632

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.89	50	15408	952	97.56	0.2165	0.2128	0.2778	RANDOM	52.9

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]
-0.6			-0.39		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.659
r_dihedral_angle_3_deg	16.963
r_dihedral_angle_4_deg	13.476
r_dihedral_angle_1_deg	5.853
r_angle_refined_deg	1.2
r_angle_other_deg	0.833
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.659
r_dihedral_angle_3_deg	16.963
r_dihedral_angle_4_deg	13.476
r_dihedral_angle_1_deg	5.853
r_angle_refined_deg	1.2
r_angle_other_deg	0.833
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3978
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
EPMR	phasing
PDB_EXTRACT	data extraction
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.