6IG8

Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	11 mg/mL protein, 22.5-35% PEG 4000, 0.1M Tris-HCL pH 8.5, 0.2M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.52	α = 90
b = 62.52	β = 90
c = 185.31	γ = 90

Symmetry
Space Group	P 43 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	CCD	MARMOSAIC 225 mm CCD		2011-06-12	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	59.24	99.8	0.079	0.09	0.031	18.8	8.3		35007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	100		0.524	0.524	0.592	0.2	1.4	8.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3LCO	1.8	59.24	33140	1751	99.38	0.1579	0.156	0.1922	RANDOM	20.164

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]
0.48			0.48		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.785
r_dihedral_angle_4_deg	20.04
r_dihedral_angle_3_deg	12.498
r_dihedral_angle_1_deg	6.607
r_angle_refined_deg	1.704
r_angle_other_deg	1.588
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.785
r_dihedral_angle_4_deg	20.04
r_dihedral_angle_3_deg	12.498
r_dihedral_angle_1_deg	6.607
r_angle_refined_deg	1.704
r_angle_other_deg	1.588
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	373
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
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 R01GM133198.