3LWZ

1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ) from Yersinia pestis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein solution: 5.3 mg/mL, 0.5M Sodium chloride, 0.01M TRIS-HCl pH 8.3; Screen solution: ANL-2, D1, 0.17M Sodim Acetate, 0.085M TRIS HCl pH 8.5, 25.5% PEG 4000, 15% Glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.587	α = 90
b = 90.587	β = 90
c = 216.5	γ = 120

Symmetry
Space Group	H 3

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	2010-02-10	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	1.65	30	99.9	0.057	20.4	3.8	79780	79780		-3	22.1

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)
	1.65	1.68	98.5		0.367	2.6	2.8	3916

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	1UQR	1.65	29.38	75607	75607	3991	99.89	0.15068	0.15068	0.14903	0.18186	RANDOM	20.511

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]
1.14	0.57		1.14		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.42
r_dihedral_angle_3_deg	11.035
r_dihedral_angle_4_deg	10.323
r_dihedral_angle_1_deg	4.357
r_scangle_it	4.336
r_scbond_it	2.791
r_mcangle_it	2.097
r_angle_refined_deg	1.319
r_mcbond_it	1.232
r_angle_other_deg	0.869

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.42
r_dihedral_angle_3_deg	11.035
r_dihedral_angle_4_deg	10.323
r_dihedral_angle_1_deg	4.357
r_scangle_it	4.336
r_scbond_it	2.791
r_mcangle_it	2.097
r_angle_refined_deg	1.319
r_mcbond_it	1.232
r_angle_other_deg	0.869
r_mcbond_other	0.34
r_chiral_restr	0.086
r_bond_refined_d	0.012
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	4908
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms	122

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.