5E7Z | pdb_00005e7z

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D/L-tryptophan and D-phenylalanine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NV8	PDB entry 3NV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 7.5, 1.5M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 0.25 MILLIM D-PHENYLALANINE AND 2.5 MILLIM TRYPTOPHAN

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 206.357	α = 90
b = 206.357	β = 90
c = 66.941	γ = 120

Symmetry
Space Group	P 32 2 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 315r		2012-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953700	Australian Synchrotron	MX2

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	2.33	47.55	100	4.2	12.3		71044

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 3NV8	2.4	47.55	60738	3128	99.9	0.138	0.137	0.17	0.161	0.19	RANDOM	35.17

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]
-0.02			-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.909
r_dihedral_angle_4_deg	18.09
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_1_deg	6.542
r_angle_refined_deg	2.006
r_angle_other_deg	1.21
r_chiral_restr	0.108
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.005
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	7030
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction