2PGF

Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	33% PEG 20000, 0.1 M TAPS (pH 9.0), 0.1 M Sodium phosphate (monobasic), 16% acetonitrile, 5 mM adenosine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.962	α = 90
b = 146.608	β = 90
c = 50.398	γ = 90

Symmetry
Space Group	C 2 2 21

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 325 mm CCD	mirrors	2007-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97943	SSRL	BL9-2

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	1.89	35	99.2	0.073	10.3	7.6	42835	42835			24.8

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	1.89	1.97	94.6		0.473	2.35	5.6	4009

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 2AMX	1.89	35	42786	42786	2144	98.36	0.15903	0.15903	0.15697	0.20061	RANDOM	21.575

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]
1.11			-2.13		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.375
r_dihedral_angle_4_deg	16.09
r_dihedral_angle_3_deg	11.491
r_dihedral_angle_1_deg	5.34
r_scangle_it	4.332
r_scbond_it	3.319
r_mcangle_it	2.127
r_mcbond_it	1.871
r_angle_refined_deg	1.058
r_angle_other_deg	0.806
r_mcbond_other	0.507
r_symmetry_vdw_other	0.243
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.202
r_nbtor_refined	0.175
r_nbd_other	0.17
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.118
r_nbtor_other	0.083
r_chiral_restr	0.061
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2915
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing