4CL0 | pdb_00004cl0

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y71	PDB ENTRY 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
2.8	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.003	α = 90
b = 126.003	β = 90
c = 126.003	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	3.1	44.55	100	0.11	19.9	9.8		3177		-3	39

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	3.1	3.27	100		0.35	7.6	9.7

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 2Y71	3.1	44.59	2970	137	99.9	0.13607	0.13199	0.14	0.22814	0.23	RANDOM	47.75

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	34.295
r_dihedral_angle_4_deg	13.305
r_dihedral_angle_3_deg	12.865
r_dihedral_angle_1_deg	6.56
r_scbond_it	6.425
r_mcangle_it	4.858
r_mcbond_it	2.938
r_scangle_it	2.44
r_angle_refined_deg	1.393
r_angle_other_deg	0.785
r_mcbond_other	0.553
r_symmetry_hbond_refined	0.257
r_xyhbond_nbd_refined	0.226
r_nbd_refined	0.214
r_symmetry_vdw_other	0.189
r_nbd_other	0.175
r_nbtor_refined	0.172
r_symmetry_vdw_refined	0.096
r_nbtor_other	0.085
r_chiral_restr	0.067
r_xyhbond_nbd_other	0.035
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	1051
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	14

Software

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