3L2I

1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GQN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein solution: 7.5 mG/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: ANL-2, drop D3; 0.2M Magnesium Chloride, 20% PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.919	α = 90
b = 76.909	β = 90
c = 171.854	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD	Beryllium lenses	2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.85	30	100	0.077	21.3	6.5	42861	42861		-3	21.1

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)
	1.85	1.88	99.8		0.355	4.1	4.5	2081

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GQN	1.85	28.64	40646	40646	2141	99.88	0.16982	0.16982	0.16753	0.21384	RANDOM	17.923

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]
-1.02			0.71		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.64
r_dihedral_angle_4_deg	13.483
r_dihedral_angle_3_deg	10.942
r_scangle_it	5.562
r_dihedral_angle_1_deg	3.588
r_scbond_it	3.309
r_mcangle_it	2.154
r_angle_refined_deg	1.526
r_mcbond_it	1.201
r_angle_other_deg	0.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.64
r_dihedral_angle_4_deg	13.483
r_dihedral_angle_3_deg	10.942
r_scangle_it	5.562
r_dihedral_angle_1_deg	3.588
r_scbond_it	3.309
r_mcangle_it	2.154
r_angle_refined_deg	1.526
r_mcbond_it	1.201
r_angle_other_deg	0.926
r_mcbond_other	0.331
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3895
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.