3MB8 | pdb_00003mb8

Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex with immucillin-H

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	100mM Tris, 0.2M Trimethylamine N-oxide dihydrate, 25% PEG 2000MME, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.622	α = 90
b = 159.622	β = 90
c = 53.606	γ = 120

Symmetry
Space Group	P 6

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 315r		2009-02-05	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	1.9	138.68	99.4	0.136	7.5	11.4		61484

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	1.9	1.97	94.4		0.541		7	5786

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	1.9	20	61465	3112	99.08	0.222	0.221	0.22	0.243	0.24	RANDOM	19.432

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]
-0.64	-0.32		-0.64		0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.062
r_dihedral_angle_4_deg	17.421
r_dihedral_angle_3_deg	13.641
r_dihedral_angle_1_deg	5.898
r_scangle_it	3.465
r_scbond_it	2.041
r_angle_refined_deg	1.457
r_mcangle_it	1.262
r_mcbond_it	0.674
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.062
r_dihedral_angle_4_deg	17.421
r_dihedral_angle_3_deg	13.641
r_dihedral_angle_1_deg	5.898
r_scangle_it	3.465
r_scbond_it	2.041
r_angle_refined_deg	1.457
r_mcangle_it	1.262
r_mcbond_it	0.674
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3748
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	72

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
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.