8B6M | pdb_00008b6m

Tankyrase 2 in complex with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OM1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277.15	100 mM Tris, 22% w/v PEG3350, 200 mM Li2SO4, 250 mM NaCl, 20% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.57	α = 90
b = 97.37	β = 90
c = 119.24	γ = 90

Symmetry
Space Group	C 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	PIXEL	DECTRIS PILATUS3 2M		2022-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	50	99.7	0.999	15.99	5.5		69406

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64			0.648

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7OM1	1.6	48.685	69405	3471	99.69	0.187	0.1849	0.2	0.2194	0.23	27.2

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]
-0.31			-0.679		0.989

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.806
r_dihedral_angle_3_deg	13.13
r_dihedral_angle_1_deg	6.874
r_lrange_it	6.523
r_lrange_other	6.494
r_dihedral_angle_2_deg	6.383
r_scangle_it	4.908
r_scangle_other	4.89
r_mcangle_it	3.553
r_mcangle_other	3.553
r_scbond_it	3.297
r_scbond_other	3.279
r_mcbond_it	2.496
r_mcbond_other	2.488
r_angle_refined_deg	1.874
r_angle_other_deg	0.612
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.213
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.181
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3308
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	108

Software

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