2Q7O

Structure of human purine nucleoside phosphorylase in complex with L-Immucillin-H

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	1.8 M Ammonium dihydrogen phosphate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
5.11	75.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.457	α = 90
b = 143.457	β = 90
c = 166.248	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 315		2006-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.07200	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	2.9	35	99.9	0.102	0.073	7.5	8.8	14755	14741			82

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	2.9	3	99.3		0.845	0.73	1.4	6.5	1442

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1rr6	2.9	34.54	14736	14728	745	99.94	0.218	0.218	0.216	0.262	RANDOM	71.358

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]
0.13	0.06		0.13		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.405
r_dihedral_angle_3_deg	24.583
r_dihedral_angle_4_deg	24.151
r_dihedral_angle_1_deg	12.518
r_scangle_it	4.281
r_angle_refined_deg	2.953
r_scbond_it	2.748
r_mcangle_it	2.027
r_mcbond_it	1.258
r_nbtor_refined	0.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.405
r_dihedral_angle_3_deg	24.583
r_dihedral_angle_4_deg	24.151
r_dihedral_angle_1_deg	12.518
r_scangle_it	4.281
r_angle_refined_deg	2.953
r_scbond_it	2.748
r_mcangle_it	2.027
r_mcbond_it	1.258
r_nbtor_refined	0.354
r_nbd_refined	0.321
r_symmetry_vdw_refined	0.307
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.181
r_symmetry_hbond_refined	0.101
r_bond_refined_d	0.033
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2223
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	24

Software

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

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.