6F5B | pdb_00006f5b

Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		PARP2 homology model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	12 % v/v Polypropylene glycol 400 0.1 M Na-acetate 3 % 2 propanol

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.16	α = 90
b = 84.36	β = 90
c = 95.96	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	PIXEL	DECTRIS PILATUS3 6M		2016-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.8	30	99.8	0.01	0.0212	1	11.36	4.77		13124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.93			1.797	0.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PARP2 homology model	2.8	30	12468	657	99.75	0.21127	0.20811	0.21	0.27392	0.27	RANDOM	83.666

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]
1.65			-1.22		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.643
r_dihedral_angle_4_deg	24.767
r_dihedral_angle_3_deg	19.227
r_long_range_B_refined	13.73
r_long_range_B_other	13.728
r_scangle_other	10.974
r_mcangle_it	9.822
r_mcangle_other	9.818
r_dihedral_angle_1_deg	7.76
r_scbond_it	7.343
r_scbond_other	7.341
r_mcbond_other	6.494
r_mcbond_it	6.493
r_angle_refined_deg	1.6
r_angle_other_deg	1.201
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1849
Nucleic Acid Atoms	824
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing