4O96 | pdb_00004o96

2.60 Angstrom resolution crystal structure of a protein kinase domain of type III effector NleH2 (ECs1814) from Escherichia coli O157:H7 str. Sakai

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	Native protein at 10 mg/mL crystallization: 1.6 M NH4 sulphate, 100 mM SPG buffer pH 7.0, 12% glycerol and 1% PEG 2000 MME. cryo conditions: Paratone-N oil , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.252	α = 90
b = 147.252	β = 90
c = 83.05	γ = 90

Symmetry
Space Group	P 4 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 300 mm CCD	Mirror	2012-08-18	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Be-Lenses	2012-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0000	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	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	2.6	50	99.2	0.106	14.5	6.6	28323	28323		-3	59.8

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	2.6	2.69	98.7		0.738	2.1	6.5	2767

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.6	46.61	26879	26879	1434	99.04	0.21038	0.20812	0.21	0.25288	0.25	RANDOM	59.25

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]
2.87			2.87		-5.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.588
r_dihedral_angle_3_deg	13.042
r_dihedral_angle_4_deg	9.405
r_dihedral_angle_1_deg	3.274
r_angle_refined_deg	1.669
r_angle_other_deg	1.342
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.588
r_dihedral_angle_3_deg	13.042
r_dihedral_angle_4_deg	9.405
r_dihedral_angle_1_deg	3.274
r_angle_refined_deg	1.669
r_angle_other_deg	1.342
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5136
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	31

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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 R01GM157729.