4MEI | pdb_00004mei

Crystal structure of a VirB8 Type IV secretion system machinery soluble domain from Bartonella tribocorum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	BatrA.18388.b.B2.PS01799 at 3.84 mg/mL against JCSG+ F10 1.1 M Na Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED2001 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 244429f10, unique puck ID jcp2-9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.54	α = 90
b = 61.54	β = 90
c = 126.47	γ = 90

Symmetry
Space Group	P 41 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	RAYONIX MX-300		2012-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	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	2.85	50	99.7	0.077	22.98	8.5	6185	6166		-3	56.293

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	2.85	2.92	100		0.589	3.86

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.85	44.14	6131	286	99.84	0.2003	0.198	0.2	0.2467	0.24	RANDOM	58.9129

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]
-1.1			-1.1		2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.615
r_dihedral_angle_4_deg	18.099
r_dihedral_angle_3_deg	17.994
r_dihedral_angle_1_deg	6.244
r_mcangle_it	4.383
r_mcbond_it	2.788
r_mcbond_other	2.778
r_angle_refined_deg	1.477
r_angle_other_deg	0.814
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.615
r_dihedral_angle_4_deg	18.099
r_dihedral_angle_3_deg	17.994
r_dihedral_angle_1_deg	6.244
r_mcangle_it	4.383
r_mcbond_it	2.788
r_mcbond_other	2.778
r_angle_refined_deg	1.477
r_angle_other_deg	0.814
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1092
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.