6HQZ

Crystal structure of the type III effector protein AvrRpt2 from Erwinia amylovora, a C70 family cysteine protease

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	9	293	100 mM TRIS-HCL pH 9.0 10% glycerol, 100 mM sodium cacodylate, 15% PEG 6K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.313	α = 90
b = 63.884	β = 90
c = 85.983	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 2M		2014-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.064	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	51.32	99.02	0.054	13.4	2.8		28980

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	94.76		0.664

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	1.8	51.32	28980	1536	99.02	0.2106	0.20944	0.23315	RANDOM	39.225

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]
-2.94			2.52		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.661
r_dihedral_angle_4_deg	18.555
r_dihedral_angle_3_deg	14.917
r_dihedral_angle_1_deg	7.023
r_long_range_B_refined	4.143
r_long_range_B_other	4.118
r_scangle_other	2.393
r_mcangle_it	1.888
r_mcangle_other	1.888
r_angle_refined_deg	1.865
r_scbond_other	1.525
r_scbond_it	1.524
r_mcbond_it	1.258
r_mcbond_other	1.257
r_angle_other_deg	1.133
r_chiral_restr	0.12
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2454
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing