3PGJ

2.49 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295	Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The Classic suite H3 (#87) condition (0.2 M Ammonium acetate, 0.1 M tri-Sodium citrate pH 5.6, 30 % (w/v) PEG4000). Crystal was soaked in 25 mM shikimate. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.527	α = 90
b = 83.657	β = 93.51
c = 79.585	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD	Be-Lenses/Diamond Laue Mono	2010-10-20	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	2.5	30	100	0.058	20.77	3.8	34293	34293		-3

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		0.525	2.41	3.8	1679

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3O8Q	2.49	28.8	32555	32555	1723	98.68	0.19609	0.19338	0.24711	RANDOM	59.66

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]
-1.5		0.58	0.42		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.359
r_dihedral_angle_3_deg	5.85
r_dihedral_angle_4_deg	4.198
r_scangle_it	3.103
r_scbond_it	1.848
r_angle_refined_deg	1.416
r_mcangle_it	1.132
r_dihedral_angle_1_deg	0.938
r_angle_other_deg	0.825
r_mcbond_it	0.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.359
r_dihedral_angle_3_deg	5.85
r_dihedral_angle_4_deg	4.198
r_scangle_it	3.103
r_scbond_it	1.848
r_angle_refined_deg	1.416
r_mcangle_it	1.132
r_dihedral_angle_1_deg	0.938
r_angle_other_deg	0.825
r_mcbond_it	0.578
r_mcbond_other	0.107
r_chiral_restr	0.083
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8261
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	48

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.