3N59 | pdb_00003n59

Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DHQ	PDB entry 2dhq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		290	MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 mg/mL protein incubated with 1.5-fold M excess of ligand, 15% PEG monomethyl ether 2,000, 0.075 M KBr, 25 mM Tris, 50 mM NaCl, 0.5 mM DTT, 0.5 mM EDTA, pH 7.5 in microbatch plates covered with 5 mL Als oil, Microbatch, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.988	α = 90
b = 137.334	β = 95.98
c = 148.101	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	ADSC QUANTUM 315		2007-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97856	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.51	50	95.11			124512	124512	-3	-3

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 2dhq	2.52	50	118244	6267	95.13	0.20008	0.19754	0.2	0.24779	0.25	RANDOM	37.126

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]
0.12		0.88	0.32		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.675
r_dihedral_angle_3_deg	13.862
r_dihedral_angle_4_deg	10.386
r_dihedral_angle_1_deg	4.559
r_angle_refined_deg	0.882
r_scangle_it	0.518
r_mcangle_it	0.366
r_scbond_it	0.299
r_nbtor_refined	0.29
r_mcbond_it	0.204
r_symmetry_vdw_refined	0.19
r_nbd_refined	0.159
r_xyhbond_nbd_refined	0.088
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24621
Nucleic Acid Atoms
Solvent Atoms	1604
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling