4O3V

Crystal structure of a VirB8-like protein of type IV secretion system from Rickettsia typhi

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	RityA.18390.a.B2 PS01633 at 11.2 mg/mL against CSHT A2, 0.4 M potassium sodium tartrate, cryo-protected with Al's oil, crystal grew over 7 months, crystal tracking ID 250519a2, unique puck ID zuk7-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.68	α = 90
b = 117.68	β = 90
c = 83.82	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	ADSC QUANTUM 315r		2013-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	1.95	50	100	0.065	24.26	9.6		43393		-3	30.753

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	1.95	2	100		0.477	4.15

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	50	43389	2182	99.97	0.1667	0.1656	0.1892	RANDOM	31.9189

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]
-1.07			-1.07		2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.052
r_dihedral_angle_4_deg	22.704
r_dihedral_angle_3_deg	12.745
r_dihedral_angle_1_deg	6.865
r_mcangle_it	3.16
r_mcbond_it	2.009
r_mcbond_other	2.006
r_angle_refined_deg	1.464
r_angle_other_deg	0.805
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.052
r_dihedral_angle_4_deg	22.704
r_dihedral_angle_3_deg	12.745
r_dihedral_angle_1_deg	6.865
r_mcangle_it	3.16
r_mcbond_it	2.009
r_mcbond_other	2.006
r_angle_refined_deg	1.464
r_angle_other_deg	0.805
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2226
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	10

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 National Science Foundation (DBI-1832184), 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 R01GM133198.