3SII | pdb_00003sii

The X-ray crystal structure of poly(ADP-ribose) glycohydrolase bound to the inhibitor ADP-HPD from Thermomonospora curvata

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SIH	PDB ENTRY 3SIH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SITTING DROP, VAPOR DIFFUSION	9		10% PEG6000, 0.1 M Bicine, pH 9.0, SITTING DROP, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2	38.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.27	α = 90
b = 44.22	β = 90
c = 50.15	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 4		2011-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.392	31.688	99.7			44399	44385

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 3SIH	1.48	31.688	1.38	44399	44385	1975	99.7	0.165	0.1634	0.16	0.1964	0.19	RANDOM	20.3848

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]
2.1917			-0.8951		-1.2966

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.221
f_angle_d	1.115
f_chiral_restr	0.067
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2028
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	35

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing

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.