2R9Q | pdb_00002r9q

Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	0.2M CaCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.693	α = 90
b = 129.042	β = 108.75
c = 85.559	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	ADSC QUANTUM 315	mirrors	2007-08-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940, 0.97960	APS	19-ID

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	46.78	93.9	0.099	17.1	4.1	73588	69099		2	57

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	2.26	53.36		0.647	0.8	1.7	5433

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.2	46.78	69099	69099	690	93.9	0.1898	0.1898	0.18904	0.22	0.26949	0.29	RANDOM	56.968

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]
0.19		-0.38	-0.12		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.399
r_dihedral_angle_4_deg	17.045
r_dihedral_angle_3_deg	16.596
r_dihedral_angle_1_deg	7.218
r_scangle_it	3.741
r_scbond_it	2.579
r_mcangle_it	1.851
r_angle_refined_deg	1.521
r_mcbond_it	1.153
r_angle_other_deg	1.057
r_mcbond_other	0.355
r_nbd_other	0.207
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.18
r_symmetry_vdw_other	0.18
r_xyhbond_nbd_other	0.174
r_nbtor_refined	0.172
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.088
r_nbtor_other	0.087
r_bond_refined_d	0.015
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	10146
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing