2FLT | pdb_00002flt

The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S0Y	trans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	equal amounts of protein solution (10 mg/mL) and well solution containing 1.6 M potassium sodium phosphate and 100 mM HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.457	α = 90
b = 59.457	β = 90
c = 57.909	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MACSCIENCE	mirrors	2004-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	30	100	0.103	19.8		6850	6850	2	2	5.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.2	100		0.355	5.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	trans-3-chloroacrylic acid dehalogenase (CaaD, PDB ID: 1S0Y)	2.1	28.96	6850	6850	327	99.9	0.204	0.1949	0.226	0.2234	RANDOM	16

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]
1.54	2.85		1.54		-3.08

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.1
c_scangle_it	2.68
c_scbond_it	1.79
c_mcangle_it	1.69
c_mcbond_it	1.41
c_angle_deg	1.3
c_improper_angle_d	0.64
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	890
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.