4FR5

Crystal Structure of Shikimate Dehydrogenase (aroE) Y210S 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, 36% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.507	α = 90
b = 88.523	β = 90
c = 118.185	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 210	mirrors	2012-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	1.0000	NSRRC	BL13C1

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	2.2	30	98.7	0.081	11.3	5.6		25263

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	2.2	2.28	95.6		0.462	4	5.6	2412

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	2.2	30	25076	1218	98.26	0.1965	0.1947	0.2308	RANDOM	29.6217

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]
-1.7			3.38		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.078
r_dihedral_angle_3_deg	20.953
r_dihedral_angle_4_deg	19.098
r_dihedral_angle_1_deg	7.871
r_scangle_it	5.381
r_scbond_it	3.397
r_mcangle_it	2.326
r_angle_refined_deg	1.419
r_mcbond_it	1.292
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.078
r_dihedral_angle_3_deg	20.953
r_dihedral_angle_4_deg	19.098
r_dihedral_angle_1_deg	7.871
r_scangle_it	5.381
r_scbond_it	3.397
r_mcangle_it	2.326
r_angle_refined_deg	1.419
r_mcbond_it	1.292
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

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.