8RCX | pdb_00008rcx

Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the drug candidate alpibectir

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:alpibectir ratio 1:1, in situ proteolysis with subtilisin, temperature 293K, vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.313	α = 90
b = 115.313	β = 90
c = 70.713	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	1.494	19.244	96.3	0.157	0.172	0.068	0.977	6.5	6.2		78828

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	1.494	1.535	92.4		0.88	0.965	0.387	0.106	2	6.4

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	1.494	19.244	78828	3979	91.009	0.181	0.1798	0.181	0.2043	0.1819	18.895

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]
-0.005	-0.003		-0.005		0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.699
r_dihedral_angle_3_deg	14.102
r_dihedral_angle_2_deg	11.056
r_dihedral_angle_1_deg	6.849
r_lrange_it	6.751
r_lrange_other	6.744
r_scangle_it	6.079
r_scangle_other	6.078
r_scbond_it	4.222
r_scbond_other	4.221
r_mcangle_it	3.161
r_mcangle_other	3.16
r_mcbond_it	2.267
r_mcbond_other	2.264
r_angle_refined_deg	2.129
r_angle_other_deg	0.681
r_nbd_other	0.302
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.187
r_xyhbond_nbd_other	0.134
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3166
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	44

Software

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