4H3D

1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 7.5mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3. Screen: 0.1M MES pH 6.5, 25% (v/v) PEG 550 MME. VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.275	α = 90
b = 138.688	β = 90.01
c = 66.315	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 300 mm CCD	Beryllium lenses	2009-11-25	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	1.95	30	99.8	0.067	17.4	3.8	79221	79221		-3	24.7

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	1.95	1.98	99.6		0.458	3.1	3.8	3903

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 3JS3	1.95	27.64	74846	74846	4014	99.75	0.15788	0.15788	0.15561	0.19936	RANDOM	24.372

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]
1.09		-0.21	0.5		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.274
r_dihedral_angle_4_deg	12.156
r_dihedral_angle_3_deg	10.365
r_scangle_it	5.469
r_scbond_it	3.474
r_dihedral_angle_1_deg	3.469
r_mcangle_it	2.091
r_angle_other_deg	1.974
r_angle_refined_deg	1.325
r_mcbond_it	1.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.274
r_dihedral_angle_4_deg	12.156
r_dihedral_angle_3_deg	10.365
r_scangle_it	5.469
r_scbond_it	3.474
r_dihedral_angle_1_deg	3.469
r_mcangle_it	2.091
r_angle_other_deg	1.974
r_angle_refined_deg	1.325
r_mcbond_it	1.238
r_mcbond_other	0.42
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8036
Nucleic Acid Atoms
Solvent Atoms	817
Heterogen Atoms	94

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 National Science Foundation (DBI-1832184), 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.