3SEF | pdb_00003sef

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

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 6.8 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Soak: 5 mM NADPH, 5 mM dehydroshikimate. Crystallization: PEGsII (B11: 0.2 M Na acetate, 0.1 M HEPES pH 7.5, 20 % (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	38.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.03	α = 90
b = 86.079	β = 92.85
c = 81.018	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 300 mm CCD	Be-Lenses	2010-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	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	2.4	30	99.9	0.055	18.92	3.8	41040	41040		-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)
1	2.4	2.44	100		0.57	2.31	3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3PGJ	2.4	29.48	38956	38956	2059	99.7	0.23666	0.23459	0.24	0.2756	0.28	RANDOM	57.938

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]
-0.19		1.04	1.64		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.844
r_dihedral_angle_3_deg	2.834
r_scangle_it	2.49
r_dihedral_angle_4_deg	1.965
r_scbond_it	1.481
r_angle_refined_deg	1.267
r_mcangle_it	1.087
r_angle_other_deg	0.797
r_mcbond_it	0.573
r_dihedral_angle_1_deg	0.45
r_chiral_restr	0.117
r_mcbond_other	0.084
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8076
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	120

Software

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