4M3D

Rapid and efficient design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging and linking approaches

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	1.4-1.65 M ammonium sulfate, 15% glycerol, 0.1 M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.482	α = 90
b = 120.482	β = 90
c = 33.768	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	MARMOSAIC 225 mm CCD		2011-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.9	42.597	99.5	0.097	18	7.9	20174	20174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	98		0.804	0.804	1	8	2848

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	42.597	20136	1025	100	0.1754	0.1727	0.2267	RANDOM	23.9804

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.727
r_dihedral_angle_4_deg	16.441
r_dihedral_angle_3_deg	14.137
r_scangle_it	7.01
r_dihedral_angle_1_deg	5.146
r_scbond_it	4.896
r_mcangle_it	2.903
r_rigid_bond_restr	2.809
r_mcbond_it	1.905
r_angle_refined_deg	1.786

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.727
r_dihedral_angle_4_deg	16.441
r_dihedral_angle_3_deg	14.137
r_scangle_it	7.01
r_dihedral_angle_1_deg	5.146
r_scbond_it	4.896
r_mcangle_it	2.903
r_rigid_bond_restr	2.809
r_mcbond_it	1.905
r_angle_refined_deg	1.786
r_chiral_restr	0.127
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1497
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XSCALE	data scaling

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 R01GM133198.