8D23 | pdb_00008d23

Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT529

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	294	100 mM Tris-HCl pH 8.5, 9.5-10% w/v PEG 8000, and 500 mM (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.826	α = 90
b = 174.826	β = 90
c = 123.721	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		2018-06-30	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	2.14	50	99.6	0.102	0.992	16.5	6.4		39393		2.1

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	2.14	2.19			0.584	0.893

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3R1K	2.14	41.27	37386	2006	98.82	0.1852	0.1838	0.19	0.2111	0.22	RANDOM	32.707

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]
-1.3	-0.65		-1.3		4.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.449
r_dihedral_angle_3_deg	13.198
r_dihedral_angle_4_deg	12.767
r_dihedral_angle_1_deg	6.917
r_angle_other_deg	2.359
r_angle_refined_deg	1.696
r_chiral_restr	0.083
r_bond_other_d	0.035
r_bond_refined_d	0.011
r_gen_planes_other	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.449
r_dihedral_angle_3_deg	13.198
r_dihedral_angle_4_deg	12.767
r_dihedral_angle_1_deg	6.917
r_angle_other_deg	2.359
r_angle_refined_deg	1.696
r_chiral_restr	0.083
r_bond_other_d	0.035
r_bond_refined_d	0.011
r_gen_planes_other	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3047
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.