3OKF

2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 3.5 mGr/mL 0.01M Tris-HCL pH 8.3, 1mM Dehydroquinate (DHQ); Screen: Classics II (B6), 0.49M Sodium phosphate, 0.91M Potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.14	α = 90
b = 80.14	β = 90
c = 262.965	γ = 90

Symmetry
Space Group	P 43 21 2

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 300 mm CCD	Beryllium lenses	2010-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	30	100	0.078	19.7	5.5	30764	30764		-3	52.5

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)
	2.5	2.54	100		0.517	2.7	5.6	1480

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	3CLH	2.5	29.62	29101	29101	1549	99.88	0.18379	0.18379	0.18168	0.2228	RANDOM	41.904

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]
2.18			2.18		-4.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.356
r_dihedral_angle_4_deg	9.803
r_dihedral_angle_3_deg	9.141
r_scangle_it	4.033
r_scbond_it	2.484
r_dihedral_angle_1_deg	2.198
r_mcangle_it	1.62
r_angle_refined_deg	1.295
r_mcbond_it	0.845
r_angle_other_deg	0.823

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.356
r_dihedral_angle_4_deg	9.803
r_dihedral_angle_3_deg	9.141
r_scangle_it	4.033
r_scbond_it	2.484
r_dihedral_angle_1_deg	2.198
r_mcangle_it	1.62
r_angle_refined_deg	1.295
r_mcbond_it	0.845
r_angle_other_deg	0.823
r_mcbond_other	0.17
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5407
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	116

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 National Science Foundation (DBI-1832184), 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 R01GM133198.