3JS3

Crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent reaction intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QFE	PDB entry 1QFE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein solution: 7.5mg/mL, 0.25M NaCl, 1mM 3-dehydroshikimate, Tris-HCl pH 8.3. Screen solution: 0.2M Magnesium chloride, 0.1M Tris-HCl pH 7.0, 10% w/v PEG 8000 , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.472	α = 90
b = 139.619	β = 90.63
c = 66.774	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 225 mm CCD	Diamond	2009-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	99.9	0.066	17.3	3.8	55938	55938		-3	44.6

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	2.24	100		0.614	2.2	3.8	2854

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1QFE	2.2	29.55	53068	53068	2839	99.76	0.19161	0.19161	0.18889	0.24147	RANDOM	21.947

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]
0.28		-0.21	1.3		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.985
r_dihedral_angle_4_deg	12.843
r_dihedral_angle_3_deg	11.071
r_scangle_it	4.556
r_scbond_it	3.038
r_dihedral_angle_1_deg	2.732
r_mcangle_it	1.758
r_angle_refined_deg	1.537
r_mcbond_it	0.962
r_angle_other_deg	0.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.985
r_dihedral_angle_4_deg	12.843
r_dihedral_angle_3_deg	11.071
r_scangle_it	4.556
r_scbond_it	3.038
r_dihedral_angle_1_deg	2.732
r_mcangle_it	1.758
r_angle_refined_deg	1.537
r_mcbond_it	0.962
r_angle_other_deg	0.904
r_mcbond_other	0.267
r_chiral_restr	0.094
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	8032
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	44

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.