3NUD | pdb_00003nud

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

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
3.96	68.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.65	α = 90
b = 204.65	β = 90
c = 66.61	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	123	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC BLUE MIRRORS	2005-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.542

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	3	39.6	97.2	0.164	5.6	2.63	31363	31363			36.2

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	3	3.077	97.2		0.344	3	2.68	31363

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	3	39.55	29566	1574	96.5	0.21517	0.21227	0.22	0.2694	0.27	RANDOM	32.676

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]
0.63	0.32		0.63		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.469
r_dihedral_angle_4_deg	15.204
r_dihedral_angle_3_deg	14.952
r_dihedral_angle_1_deg	5.488
r_scangle_it	5.143
r_scbond_it	3.124
r_mcangle_it	2.447
r_mcbond_it	1.333
r_angle_other_deg	1.27
r_angle_refined_deg	1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.469
r_dihedral_angle_4_deg	15.204
r_dihedral_angle_3_deg	14.952
r_dihedral_angle_1_deg	5.488
r_scangle_it	5.143
r_scbond_it	3.124
r_mcangle_it	2.447
r_mcbond_it	1.333
r_angle_other_deg	1.27
r_angle_refined_deg	1.16
r_mcbond_other	0.188
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6756
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	85

Software

Software
Software Name	Purpose
CrystalClear	data collection
CCP4	model building
REFMAC	refinement
d*TREK	data reduction
d*TREK	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.