6ZGN

Crystal structure of VirB8-like OrfG central domain of Streptococcus thermophilus ICESt3; a putative assembly factor of a gram positive conjugative Type IV secretion system.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Ammonium sulfate; 2M Tris pH 8.5; 100 mM

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.162	α = 90
b = 50.162	β = 90
c = 120.883	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	PIXEL	DECTRIS EIGER X 9M		2019-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.75	46.331	100	0.027	0.028	0.006	1	67.5	25.1		16372			29.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		0.499	0.511	0.105	0.975		23.8

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.75	46.331	16309	835	99.951	0.2	0.1996	0.2081	Random	35.347

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]
0.701			0.701		-1.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	40.476
r_dihedral_angle_2_deg	34.206
r_dihedral_angle_3_deg	15.399
r_lrange_other	8.636
r_lrange_it	8.635
r_scangle_it	7.368
r_scangle_other	7.368
r_dihedral_angle_1_deg	6.107
r_scbond_other	5.303
r_scbond_it	5.281
r_mcangle_other	4.545
r_mcangle_it	4.522
r_mcbond_other	3.596
r_mcbond_it	3.555
r_angle_other_deg	1.784
r_angle_refined_deg	1.635
r_symmetry_nbd_refined	0.387
r_nbd_refined	0.226
r_nbtor_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.2
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_other	0.176
r_nbd_other	0.175
r_symmetry_nbtor_other	0.1
r_chiral_restr	0.088
r_bond_other_d	0.021
r_bond_refined_d	0.014
r_gen_planes_other	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	842
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing