5E40 | pdb_00005e40

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site

X-RAY DIFFRACTION

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	298	0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and 24 hours before crystal freezing, respectively

Crystal Properties
Matthews coefficient	Solvent content
4	69.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.451	α = 90
b = 205.451	β = 90
c = 66.803	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 210r		2012-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.05	19.85	99.9	0.143	0.056	0.997	11.8	7.5		101083

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	100		1.026	0.398	0.608	2.1	7.5	5007

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	2.05	19.85	96017	5046	99.86	0.1948	0.1941	0.19	0.207	0.2	RANDOM	27.469

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]
2.44			2.44		-4.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.373
r_dihedral_angle_4_deg	15.924
r_dihedral_angle_3_deg	12.761
r_dihedral_angle_1_deg	5.242
r_mcangle_it	2.339
r_mcbond_it	1.279
r_mcbond_other	1.279
r_angle_refined_deg	1.155
r_angle_other_deg	0.806
r_chiral_restr	0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.373
r_dihedral_angle_4_deg	15.924
r_dihedral_angle_3_deg	12.761
r_dihedral_angle_1_deg	5.242
r_mcangle_it	2.339
r_mcbond_it	1.279
r_mcbond_other	1.279
r_angle_refined_deg	1.155
r_angle_other_deg	0.806
r_chiral_restr	0.061
r_gen_planes_refined	0.009
r_bond_refined_d	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7045
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	54

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.