5QI3 | pdb_00005qi3

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000475a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	80 mM KBr, 30 % PEG2kMME

Crystal Properties
Matthews coefficient	Solvent content
2	38.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.493	α = 90
b = 41.533	β = 90
c = 110.868	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 PILATUS 6M		2017-03-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.05	29.29	80.2	0.065	0.071	0.028	0.996	22.9	4.9		60056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.08	14.8		0.137	0.194	0.137	0.931		1.1	795

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	FOURIER SYNTHESIS	THROUGHOUT	4ABL	1.05	55.5	56943	3047	79.94	0.1408	0.1399	0.14	0.1576	0.16	RANDOM	12.445

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]
0.62			-0.47		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.012
r_dihedral_angle_4_deg	20.533
r_sphericity_free	19.395
r_dihedral_angle_3_deg	10.702
r_sphericity_bonded	6.753
r_dihedral_angle_1_deg	5.725
r_angle_refined_deg	1.39
r_mcangle_it	1.237
r_rigid_bond_restr	1.023
r_angle_other_deg	0.942

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.012
r_dihedral_angle_4_deg	20.533
r_sphericity_free	19.395
r_dihedral_angle_3_deg	10.702
r_sphericity_bonded	6.753
r_dihedral_angle_1_deg	5.725
r_angle_refined_deg	1.39
r_mcangle_it	1.237
r_rigid_bond_restr	1.023
r_angle_other_deg	0.942
r_mcbond_it	0.904
r_mcbond_other	0.901
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1380
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.