2Y77 | pdb_00002y77

Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-3-(benzo(b)thiophen-2-ylmethoxy)-1,4,5- trihydroxy-2-(thiophen-2-ylmethyl)cyclohex-2-enecarboxylate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H0S	PDB ENTRY 1H0S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE, 12.5 MM SODIUM (1R,4S,5R)- 3-(1-BENZOTHIOPHEN-2-YLMETHOXY)-1,4,5-TRIHYDROXY-2-(THIOPHEN- 2-YLMETHYL) CYCLOHEX-2-ENE-1-CARBOXYLATE.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.8	α = 90
b = 125.8	β = 90
c = 125.8	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	CCD	ADSC QUANTUM 210r	1 - A RD COATED FLAT MIRROR - 2 - A RD COATED TOROIDAL MIRROR	2009-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16		ESRF	BM16

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	1.4	31.5	94.3	0.06	7.5	7.5		30571			16.8

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	1.4	1.48	64.9		0.4	2	1.6

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	PDB ENTRY 1H0S	1.5	20	24982	1330	99.92	0.16244	0.16133	0.17	0.18388	0.19	RANDOM	11.457

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	30.486
r_dihedral_angle_4_deg	13.597
r_dihedral_angle_3_deg	12.577
r_dihedral_angle_1_deg	5.538
r_scangle_it	3.451
r_scbond_it	2.327
r_mcangle_it	1.544
r_angle_refined_deg	1.539
r_mcbond_it	0.995
r_rigid_bond_restr	0.923
r_angle_other_deg	0.883
r_mcbond_other	0.321
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1016
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing