3LB0 | pdb_00003lb0

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Citrate Bound to the Active Site.

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	4.2	295	Protein solution:7.5 mG/mL, 0.01M Comenic acid, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3) Screen solution: JCSG+ (condition 25), 0.2M Sodium Chloride, 0.1M Phosphate-citrate (pH 4.2), 20% w/v PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.888	α = 93.95
b = 45.853	β = 101.19
c = 80.816	γ = 105.49

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	2009-12-21	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	1.65	30	93.9	0.033	21.2	2	56117	56117		-3	18.8

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)
	1.65	1.68	95.4		0.13	5.5	1.8	2889

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	1.65	26.3	53255	53255	2829	93.86	0.16249	0.16249	0.16048	0.17	0.20071	0.21	RANDOM	17.109

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]
-0.09	0.75	-0.12	2.01	-0.04	-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.065
r_dihedral_angle_4_deg	14.159
r_dihedral_angle_3_deg	10.149
r_scangle_it	4.833
r_dihedral_angle_1_deg	3.505
r_scbond_it	2.939
r_mcangle_it	1.948
r_angle_refined_deg	1.471
r_mcbond_it	1.145
r_angle_other_deg	0.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.065
r_dihedral_angle_4_deg	14.159
r_dihedral_angle_3_deg	10.149
r_scangle_it	4.833
r_dihedral_angle_1_deg	3.505
r_scbond_it	2.939
r_mcangle_it	1.948
r_angle_refined_deg	1.471
r_mcbond_it	1.145
r_angle_other_deg	0.899
r_mcbond_other	0.337
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4333
Nucleic Acid Atoms
Solvent Atoms	600
Heterogen Atoms	24

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.