3O1N | pdb_00003o1n

1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein: 7.5 mg/mL, 0.5M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M Tris, pH 8.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.433	α = 104.23
b = 46.476	β = 97.5
c = 55.79	γ = 98.7

Symmetry
Space Group	P 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	Beryllium lenses	2010-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	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	1.03	30	92.7	0.068	15	4.3	196964	196964		-3	10.2

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)
	1.03	1.05	84.9		0.333	3.7	3.4	8952

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	3L2I	1.03	26.62	187094	187094	9868	92.63	0.14132	0.14132	0.14024	0.15	0.16161	0.17	RANDOM	10.933

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]
-0.62	0.61	-0.79	1.22	-0.89	-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.151
r_dihedral_angle_4_deg	13.106
r_dihedral_angle_3_deg	10.697
r_dihedral_angle_1_deg	5.494
r_scangle_it	4.922
r_scbond_it	3.419
r_mcangle_it	2.482
r_mcbond_it	1.696
r_angle_refined_deg	1.464
r_rigid_bond_restr	1.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.151
r_dihedral_angle_4_deg	13.106
r_dihedral_angle_3_deg	10.697
r_dihedral_angle_1_deg	5.494
r_scangle_it	4.922
r_scbond_it	3.419
r_mcangle_it	2.482
r_mcbond_it	1.696
r_angle_refined_deg	1.464
r_rigid_bond_restr	1.445
r_angle_other_deg	0.886
r_mcbond_other	0.638
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3785
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	5

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.