6VUR | pdb_00006vur

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT366

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R1K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	100 mM Tris-HCl pH 8.5 adjusted at room temperature, 10% w/v PEG 8000, and 500 mM (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.776	α = 90
b = 174.776	β = 90
c = 123.268	γ = 120

Symmetry
Space Group	H 3 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 16M		2018-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	50	99.9	0.164	0.995	16.6	7.4		36796

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24			1	0.786

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3R1K	2.2	40	34764	1805	99.67	0.1815	0.18	0.2101	RANDOM	33.306

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]
-1.45	-0.72		-1.45		4.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.352
r_dihedral_angle_4_deg	17.908
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_1_deg	6.646
r_angle_refined_deg	1.269
r_angle_other_deg	1.189
r_chiral_restr	0.053
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.352
r_dihedral_angle_4_deg	17.908
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_1_deg	6.646
r_angle_refined_deg	1.269
r_angle_other_deg	1.189
r_chiral_restr	0.053
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.