2NUD

The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NH1	PDB entry 1NH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	1:2-3 ratio of protein to peptide with AvrB at ~12 mg/ml mixed with an equal volume of well solution (100 mM Tris, pH 7.5, 20-30% PEG 550 MME), VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.884	α = 90
b = 58.166	β = 89.92
c = 119.767	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Confocal "Blue"	2004-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	99	88.8	0.109	11		29016	29016	1	1	36.2

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)
	2.2	2.28	72.7		0.437	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 1NH1	2.3	19.96	1.5	28265	26385	1273	93.2	0.21	0.21	0.26	RANDOM	32.1

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]
2.31		-0.42	0.24		-2.54

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.9
c_scangle_it	4.29
c_scbond_it	3.1
c_mcangle_it	3.05
c_mcbond_it	1.96
c_angle_deg	1.2
c_improper_angle_d	0.75
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5012
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	44

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data collection
HKL-3000	data reduction
HKL-3000	data scaling
AMoRE	phasing