3ENZ | pdb_00003enz

Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NW4	PDB entry 1NW4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	4.0M Sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.82	α = 90
b = 177.82	β = 90
c = 253.868	γ = 90

Symmetry
Space Group	I 41 2 2

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 225 mm CCD		2007-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.196	SRS	PX10.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.03	145.86	99.4	0.106	0.106	18.5	10.7	129248	129248		2	33.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.1	99.8		0.556	0.556	2.7	8

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1NW4	2.03	145.86	129248	122746	6502	99.37	0.16201	0.16035	0.16035	0.16	0.19325	0.19	RANDOM	16.879

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]
-0.08			-0.08		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.925
r_dihedral_angle_4_deg	20.515
r_dihedral_angle_3_deg	13.305
r_dihedral_angle_1_deg	6.698
r_scangle_it	3.584
r_scbond_it	2.28
r_angle_refined_deg	1.396
r_mcangle_it	1.235
r_mcbond_it	0.72
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.925
r_dihedral_angle_4_deg	20.515
r_dihedral_angle_3_deg	13.305
r_dihedral_angle_1_deg	6.698
r_scangle_it	3.584
r_scbond_it	2.28
r_angle_refined_deg	1.396
r_mcangle_it	1.235
r_mcbond_it	0.72
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.121
r_metal_ion_refined	0.119
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11226
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	221

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.