4CIX

Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with(1R,4R,5R)-1,4,5-trihydroxy-3-((1S)-1-hydroxy-2-phenyl) ethylcyclohex-2-en-1-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		32% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE-1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.9	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.36	α = 90
b = 126.36	β = 90
c = 126.36	γ = 90

Symmetry
Space Group	F 2 3

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 PILATUS 6M	CYLINDRICAL GRAZING INCIDENCE MIRROR	2013-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.9	44.67	99.3	0.11	12	4.8		3767		-3	25.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.35	4.6	5.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2Y71	2.9	38.13	3589	168	98.79	0.15348	0.15187	0.18867	RANDOM	28.072

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	31.17
r_dihedral_angle_4_deg	15.656
r_dihedral_angle_3_deg	14.848
r_dihedral_angle_1_deg	6.675
r_scbond_it	4.693
r_mcangle_it	2.646
r_mcbond_it	1.592
r_scangle_it	1.333
r_angle_refined_deg	1.323
r_angle_other_deg	0.853
r_mcbond_other	0.253
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.206
r_xyhbond_nbd_refined	0.192
r_nbd_other	0.173
r_symmetry_vdw_refined	0.172
r_nbtor_refined	0.171
r_symmetry_vdw_other	0.168
r_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1006
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALE	data scaling
MOLREP	phasing