3PHC | pdb_00003phc

Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	291	0.1M sodium formate, 10% PEG 3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.197	α = 67.71
b = 77.371	β = 73.62
c = 92.197	γ = 86.03

Symmetry
Space Group	P 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			2008-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	20	94.2	0.059	11.2	3.2		95778

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	2.07	78.9		0.152		3.1	8048

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	20	95775	4781	93.76	0.1995	0.1977	0.2	0.2349	0.24	RANDOM	29.7476

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]
0.32	2.35	1.48	0.38	2.21	-3.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.929
r_dihedral_angle_4_deg	17.061
r_dihedral_angle_3_deg	14.274
r_dihedral_angle_1_deg	6.051
r_scangle_it	2.72
r_scbond_it	1.678
r_angle_refined_deg	1.317
r_mcangle_it	1.055
r_mcbond_it	0.559
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.929
r_dihedral_angle_4_deg	17.061
r_dihedral_angle_3_deg	14.274
r_dihedral_angle_1_deg	6.051
r_scangle_it	2.72
r_scbond_it	1.678
r_angle_refined_deg	1.317
r_mcangle_it	1.055
r_mcbond_it	0.559
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11166
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	153

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.