3NUE | pdb_00003nue

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B7O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	20MM BTP, 150MM NACL, 0.5MM TCEP, 0.005%(V/V) THESIT, 0.2MM PEP, 0.1MM MNCL2, 0.1M NA HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.712	α = 90
b = 204.712	β = 90
c = 66.264	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 315	Double-crystal, Si(111)	2005-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97929	SSRL	BL9-2

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	2.5	50	100	0.134	10.4	2.8	52344	52344

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	2.5	2.59	100		0.633	2.1	2.8	52344

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	2B7O	2.5	38.69	52324	2815	99.98	0.19101	0.18901	0.19	0.22814	0.23	RANDOM	28.181

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	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.629
r_dihedral_angle_4_deg	21.011
r_dihedral_angle_3_deg	17.228
r_dihedral_angle_1_deg	6.698
r_scangle_it	4.766
r_scbond_it	3.239
r_mcangle_it	2.144
r_angle_refined_deg	1.67
r_angle_other_deg	1.305
r_mcbond_it	1.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.629
r_dihedral_angle_4_deg	21.011
r_dihedral_angle_3_deg	17.228
r_dihedral_angle_1_deg	6.698
r_scangle_it	4.766
r_scbond_it	3.239
r_mcangle_it	2.144
r_angle_refined_deg	1.67
r_angle_other_deg	1.305
r_mcbond_it	1.249
r_mcbond_other	0.435
r_chiral_restr	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_gen_planes_other	0.013
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6871
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	121

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	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.