2ISC

Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.17 M Sodium Acetate, 25.5% PEG 4000, 0.085 M TrisHCL, 15% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.402	α = 90
b = 113.821	β = 90
c = 195.149	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	ADSC QUANTUM 315		2006-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979099	NSLS	X29A

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	2.7	30	98.1	0.133	0.116	5.1	6.9	51179	50207			50.856

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	2.7	2.8	93.8		0.636	0.594	1.72	4.4	4713

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.7	29.99	51139	50106	2549	97.98	0.20187	0.202	0.199	0.252	RANDOM	37.872

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]
-0.01			0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.414
r_dihedral_angle_3_deg	18.991
r_dihedral_angle_4_deg	14.627
r_dihedral_angle_1_deg	6.306
r_scangle_it	2.031
r_angle_refined_deg	1.438
r_scbond_it	1.268
r_mcangle_it	1.14
r_mcbond_it	0.635
r_metal_ion_refined	0.405

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.414
r_dihedral_angle_3_deg	18.991
r_dihedral_angle_4_deg	14.627
r_dihedral_angle_1_deg	6.306
r_scangle_it	2.031
r_angle_refined_deg	1.438
r_scbond_it	1.268
r_mcangle_it	1.14
r_mcbond_it	0.635
r_metal_ion_refined	0.405
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.092
r_symmetry_hbond_refined	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10721
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	154

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.