3LM2

Crystal structure of Putative kinase. (17743352) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	20.0000% polyethylene glycol 3350, 0.2000M calcium acetate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.907	α = 97.98
b = 49.598	β = 104.64
c = 57.328	γ = 109.97

Symmetry
Space Group	P 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	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-11-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.96109,0.97949,0.97936	SSRL	BL9-2

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	1.7	29.13	85.7	0.06	6.16			48619		-3	25.125

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	1.7	1.76	77.9		0.151	2.1

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	MAD	THROUGHOUT	1.7	29.13	48619	2471	94.54	0.161	0.16	0.186	RANDOM	18.481

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]
-0.76	2	0.41	3.65	1.28	-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.628
r_dihedral_angle_4_deg	14.399
r_dihedral_angle_3_deg	13.484
r_dihedral_angle_1_deg	5.576
r_scangle_it	3.591
r_scbond_it	2.243
r_angle_refined_deg	1.483
r_mcangle_it	1.43
r_angle_other_deg	0.938
r_mcbond_it	0.827

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.628
r_dihedral_angle_4_deg	14.399
r_dihedral_angle_3_deg	13.484
r_dihedral_angle_1_deg	5.576
r_scangle_it	3.591
r_scbond_it	2.243
r_angle_refined_deg	1.483
r_mcangle_it	1.43
r_angle_other_deg	0.938
r_mcbond_it	0.827
r_mcbond_other	0.239
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3358
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.