8S7L | pdb_00008s7l

Crystal structure of a double mutant of VirB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PKW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Droplet: 0.3 ul [protein (33mg/ml) in 50 mM Tris pH 8.0 + 100 mM NaCl] + 0.3 ul [reservoir] Reservoir: 50 ul [40% v/v PEG 300, 100 mM potassium phosphate citrate, pH 4.2]

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.743	α = 90
b = 89.185	β = 112.314
c = 98.424	γ = 90

Symmetry
Space Group	C 1 2 1

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 4M		2022-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

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	2.6	91.054	98.8	0.062	0.087	0.061	0.995	10.6	3.1		37215			50.28

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	2.6	2.72	99.8		0.665	0.933	0.653	0.682	1.8	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	91.054	37211	1819	98.564	0.204	0.2017	0.2053	0.2563	0.2597	86.279

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]
-2.736		-1.259	0.313		2.585

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.808
r_dihedral_angle_2_deg	16.183
r_lrange_it	15.484
r_lrange_other	15.484
r_dihedral_angle_6_deg	15.479
r_scangle_it	15.375
r_scangle_other	15.374
r_mcangle_it	12.904
r_mcangle_other	12.904
r_scbond_it	12.387
r_scbond_other	12.385
r_mcbond_it	10.727
r_mcbond_other	10.725
r_dihedral_angle_1_deg	8.758
r_angle_refined_deg	2.562
r_angle_other_deg	0.816
r_symmetry_xyhbond_nbd_refined	0.276
r_nbd_refined	0.212
r_symmetry_nbd_other	0.209
r_nbd_other	0.206
r_symmetry_nbd_refined	0.203
r_nbtor_refined	0.197
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.112
r_symmetry_xyhbond_nbd_other	0.1
r_symmetry_nbtor_other	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_ext_dist_refined_b	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5912
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing