5E4N | pdb_00005e4n

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

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	293	0.1 M TRIS-HCL, PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 5 MM D-TYROSINE FOR 24 HRS

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.739	α = 90
b = 205.739	β = 90
c = 66.644	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		2013-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953700	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	47.37	100	0.165	0.051	0.998	14.9	11.4		101243

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		1.233	0.383	0.625	2.5	11.3	5044

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	47.37	96174	5048	99.98	0.2004	0.1989	0.18	0.2287	0.2	RANDOM	31.482

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]
2.28			2.28		-4.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.946
r_dihedral_angle_4_deg	17.244
r_dihedral_angle_3_deg	13.336
r_dihedral_angle_1_deg	5.597
r_angle_refined_deg	1.452
r_angle_other_deg	0.805
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.946
r_dihedral_angle_4_deg	17.244
r_dihedral_angle_3_deg	13.336
r_dihedral_angle_1_deg	5.597
r_angle_refined_deg	1.452
r_angle_other_deg	0.805
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7000
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	60

Software

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

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.