8RCW | pdb_00008rcw

Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the lead compound SMARt751

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P9WMJ3-F1	residues 1-230

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.3 M sodium acetate trihydrate, 0.1 M Tris, pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG 500 MME, pH7.5, protein:SMART751 ratio 1:1, in situ proteolysis with subtilisin, temperature 293K, vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.332	α = 90
b = 115.332	β = 90
c = 70.987	γ = 120

Symmetry
Space Group	P 61

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 PILATUS3 6M		2023-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

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	1.692	19.295	96.5	0.17	0.179	0.056	0.997	9.6	10.1		51863

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	1.692	1.767	77.3		1.68	1.778	0.576	0.56		9.4

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	THROUGHOUT	1.692	19.295	51863	2583	86.463	0.187	0.1855	0.2	0.2168	0.22	20.15

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]
-0.035	-0.018		-0.035		0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.402
r_dihedral_angle_3_deg	14.756
r_dihedral_angle_2_deg	7.35
r_lrange_it	6.398
r_lrange_other	6.385
r_dihedral_angle_1_deg	6.362
r_scangle_it	5.347
r_scangle_other	5.346
r_scbond_other	3.496
r_scbond_it	3.494
r_mcangle_it	3.332
r_mcangle_other	3.332
r_mcbond_it	2.282
r_mcbond_other	2.28
r_angle_refined_deg	1.673
r_angle_other_deg	0.557
r_nbd_refined	0.221
r_nbd_other	0.201
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.12
r_xyhbond_nbd_refined	0.106
r_symmetry_nbd_refined	0.094
r_ncsr_local_group_1	0.088
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3172
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
autoPROC	data reduction