6VV3 | pdb_00006vv3

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1358

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		295	100 mM Tris-HCl pH 8.0 adjusted at room temperature, 7% w/v PEG 8000, and 400 mM (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
4.03	69.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.353	α = 90
b = 175.353	β = 90
c = 125.155	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		2019-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	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	2.4	50	98.9	0.111	0.994	17.9	6.2		28642

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	2.4	2.44	99.5		1.132	0.813

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	2.4	35	26765	1460	97.48	0.1874	0.1854	0.226	RANDOM	42.213

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]
-1.58	-0.79		-1.58		5.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.83
r_dihedral_angle_4_deg	17.973
r_dihedral_angle_3_deg	16.694
r_dihedral_angle_1_deg	6.638
r_angle_other_deg	2.318
r_angle_refined_deg	1.348
r_chiral_restr	0.064
r_bond_other_d	0.035
r_bond_refined_d	0.006
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.83
r_dihedral_angle_4_deg	17.973
r_dihedral_angle_3_deg	16.694
r_dihedral_angle_1_deg	6.638
r_angle_other_deg	2.318
r_angle_refined_deg	1.348
r_chiral_restr	0.064
r_bond_other_d	0.035
r_bond_refined_d	0.006
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3047
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	53

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.