6II7 | pdb_00006ii7

Crystal structure of Plasmodium falciparum adenosine deaminase C27Q+L227I mutant co-complexed with Zn ion, hypoxanthine and inosine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5	294	0.1M MMT buffer pH 5.0, 25% PEG w/v 1500

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.605	α = 90
b = 62.553	β = 90
c = 126.703	γ = 90

Symmetry
Space Group	P 21 21 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	Nonius Kappa CCD	Mirrors	2013-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.54

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	2.48	50	99.8	0.057	17.3	4.8		14322

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	2.48	2.57	99.4		0.173		2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2PGF	2.48	50	13546	716	99.76	0.1762	0.173	0.18	0.2388	0.24	RANDOM	19.314

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]
-1.46			0.92		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.119
r_dihedral_angle_3_deg	15.081
r_dihedral_angle_4_deg	13.643
r_dihedral_angle_1_deg	6.126
r_angle_refined_deg	1.552
r_angle_other_deg	0.985
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.119
r_dihedral_angle_3_deg	15.081
r_dihedral_angle_4_deg	13.643
r_dihedral_angle_1_deg	6.126
r_angle_refined_deg	1.552
r_angle_other_deg	0.985
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2890
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	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.