3VFQ | pdb_00003vfq

Human PARP14 (ARTD8, BAL2) - macro domains 1 and 2 in complex with adenosine-5-diphosphoribose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q6Z	PDB ENTRIES 3Q6Z AND 3Q71
experimental model	PDB	3Q71	PDB ENTRIES 3Q6Z AND 3Q71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20% PEG3350, 0.2M SODIUM-THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.62	α = 90
b = 59.94	β = 90
c = 144.34	γ = 90

Symmetry
Space Group	P 2 2 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 315r		2010-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93928	ESRF	ID14-4

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	2.8	50	99.9	0.175	0.132	10.1	8.3	10514	10514

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	2.8	2.87	99.7		0.805	0.652	2.3	7.6	750

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3Q6Z AND 3Q71	2.8	46.62	9462	9462	1052	100	0.23787	0.23787	0.23277	0.23	0.28305	0.28	RANDOM

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]
1.57			-3.36		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.331
r_dihedral_angle_3_deg	20.755
r_dihedral_angle_4_deg	19.068
r_dihedral_angle_1_deg	6.591
r_scangle_it	2.587
r_angle_refined_deg	1.473
r_scbond_it	1.445
r_mcangle_it	0.943
r_angle_other_deg	0.874
r_mcbond_it	0.484

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.331
r_dihedral_angle_3_deg	20.755
r_dihedral_angle_4_deg	19.068
r_dihedral_angle_1_deg	6.591
r_scangle_it	2.587
r_angle_refined_deg	1.473
r_scbond_it	1.445
r_mcangle_it	0.943
r_angle_other_deg	0.874
r_mcbond_it	0.484
r_chiral_restr	0.071
r_mcbond_other	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2873
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	36

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.