3O8Q | pdb_00003o8q

1.45 Angstrom Resolution Crystal Structure of Shikimate 5-Dehydrogenase (aroE) from Vibrio cholerae

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 6.8 mGr/mL, 0.5 Sodium cloride, 0.01M Tris-HCl pH 8.3, 10 mM Curcumin; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.871	α = 90
b = 63.146	β = 90
c = 136.842	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	2010-07-23	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	1.45	30	99.8	0.058	25.7	5.8	88234	88234		-3	16.4

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)
	1.45	1.48	100		0.549	3.2	5.6	4378

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1NYT	1.45	29.32	83518	83518	4417	99.83	0.15398	0.15398	0.15182	0.15	0.19455	0.19	RANDOM	15.218

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]
-0.3			-0.32		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.429
r_dihedral_angle_4_deg	12.621
r_dihedral_angle_3_deg	11.11
r_scangle_it	5.414
r_dihedral_angle_1_deg	4.122
r_scbond_it	3.684
r_mcangle_it	2.507
r_mcbond_other	2.198
r_rigid_bond_restr	1.875
r_mcbond_it	1.664

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.429
r_dihedral_angle_4_deg	12.621
r_dihedral_angle_3_deg	11.11
r_scangle_it	5.414
r_dihedral_angle_1_deg	4.122
r_scbond_it	3.684
r_mcangle_it	2.507
r_mcbond_other	2.198
r_rigid_bond_restr	1.875
r_mcbond_it	1.664
r_angle_refined_deg	1.539
r_angle_other_deg	0.955
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4138
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	37

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.