4DHK | pdb_00004dhk

Crystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from Burkholderia thailandensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KM3	PDB entry 3km3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.87	α = 90
b = 92.87	β = 90
c = 137.59	γ = 120

Symmetry
Space Group	H 3

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	Adjustable focus K-B pair Si plus Pt, Rh coatings	2011-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	2.05	69.44	100	0.044	22.71	4.52	27772	27763		-3	39.228

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	2.05	2.1	100		0.458	3.4	4.48	2046

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	MR	THROUGHOUT	PDB entry 3km3	2.05	69.44	27772	27761	1395	99.96	0.168	0.168	0.168	0.17	0.186	0.18	RANDOM	39.189

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.348
r_dihedral_angle_4_deg	19.154
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	6.056
r_angle_refined_deg	1.417
r_angle_other_deg	1.018
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.348
r_dihedral_angle_4_deg	19.154
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	6.056
r_angle_refined_deg	1.417
r_angle_other_deg	1.018
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2535
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

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.