4FQ8

Crystal Structure of Shikimate Dehydrogenase (aroE) Y210A Mutant from Helicobacter pylori in Complex with Shikimate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.2M sodium acetate, 0.1M Tris, 29% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.244	α = 90
b = 88.335	β = 90
c = 118.338	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	110	CCD	ADSC QUANTUM 315	mirrors	2012-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

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	2.06	30	99.7	0.075	13.3	6.4		30207

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	2.06	2.13	100		0.383	5.2	6.3	2973

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 3PHG	2.07	30	30151	1516	99.32	0.2109	0.2088	0.2507	RANDOM	28.9542

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]
-0.2			1.98		-1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.904
r_dihedral_angle_4_deg	21.361
r_dihedral_angle_3_deg	20.113
r_dihedral_angle_1_deg	7.544
r_scangle_it	5.425
r_scbond_it	3.512
r_mcangle_it	2.403
r_angle_refined_deg	1.45
r_mcbond_it	1.393
r_chiral_restr	0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.904
r_dihedral_angle_4_deg	21.361
r_dihedral_angle_3_deg	20.113
r_dihedral_angle_1_deg	7.544
r_scangle_it	5.425
r_scbond_it	3.512
r_mcangle_it	2.403
r_angle_refined_deg	1.45
r_mcbond_it	1.393
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4114
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

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 R01GM133198.