3OV5 | pdb_00003ov5

Atomic structure of the Xanthomonas citri VirB7 globular domain.

X-RAY DIFFRACTION

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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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1263	0.15161	0.1481	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