3OV5

Atomic structure of the Xanthomonas citri VirB7 globular domain.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Globular domain from NMR structure of the same protein.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	14 mg/mL protein in 5 mM Tris-Cl pH 7.5 and 25 mM sodium chloride was submitted to vapor diffusion sitting-drop crystallization trials at 291 K. Large plates appeared after one day over a reservoir solution comprising 1.4 M ammonium sulphate and 4 % (v/v) isopropyl alcohol. Reservoir solution supplemented with 25 % (v/v) glycerol was used as cryoprotectant. , VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
1.78	31.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.76	α = 90
b = 55.81	β = 90
c = 83.097	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 225 mm CCD		2009-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	0.9537	LNLS	W01B-MX2

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	1.04	30	96.3	0.068	34.8	12.1	30386	30320			5.4

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	1.04	1.08	79		0.293	5.1	8.9	2449

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Globular domain from NMR structure of the same protein.	1.04	23.81	28796	28796	1524	96.32	0.1312	0.1312	0.13014	0.15161	RANDOM	10.366

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]
0.36			-1.21		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.88
r_dihedral_angle_4_deg	15.847
r_dihedral_angle_3_deg	10.476
r_sphericity_free	7.893
r_dihedral_angle_1_deg	7.195
r_sphericity_bonded	6.875
r_scangle_it	3.281
r_scbond_it	2.675
r_mcangle_it	2.2
r_angle_refined_deg	1.69
r_mcbond_it	1.546
r_rigid_bond_restr	1.341
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.213
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	619
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling