4KIU

Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49d [5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic acid]

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	298	0.15M KBr, 30% 5000mme, pH 7.8, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.41	α = 90
b = 139.15	β = 96.6
c = 143.29	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm		2009-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97910	ESRF	ID23-1

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	2.4	142.722	97.2	0.173	5.8	2.8	142809	142809	2	2

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	2.4	2.53	93.5		0.867	0.867	0.7	2.5	20000

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.4	45.28	142809	139255	6962	95.03	0.1939	0.1902	0.2646	RANDOM	29.9535

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	34.604
r_dihedral_angle_3_deg	19.216
r_dihedral_angle_4_deg	15.975
r_dihedral_angle_1_deg	6.985
r_angle_refined_deg	1.831
r_chiral_restr	0.116
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25703
Nucleic Acid Atoms
Solvent Atoms	761
Heterogen Atoms	506

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
AMoRE	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 R01GM133198.