6TKM | pdb_00006tkm

Tankyrase 2 in complex with an inhibitor (OM-1800)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NOB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.15	7.5-25% PEG 6000, Bicine, pH = 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.32	α = 90
b = 77.41	β = 90
c = 148.68	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 EIGER2 XE 16M		2018-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979500	Diamond	I04

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	2.7	50	98.4	0.974	5.09	3.4339		25517

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	2.7	2.77			0.627	1.21

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	5NOB	2.7	29.735	13994	700	99.403	0.239	0.237	0.24	0.2714	0.27	37.872

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]
2.141			3.474		-5.615

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.309
r_dihedral_angle_3_deg	15.877
r_dihedral_angle_4_deg	13.564
r_dihedral_angle_1_deg	6.322
r_lrange_it	4.751
r_lrange_other	4.751
r_mcangle_it	2.997
r_mcangle_other	2.997
r_scangle_it	2.34
r_scangle_other	2.34
r_mcbond_it	1.657
r_mcbond_other	1.657
r_chiral_restr_other	1.501
r_scbond_it	1.297
r_scbond_other	1.297
r_angle_refined_deg	1.275
r_angle_other_deg	1.165
r_nbd_other	0.227
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_refined	0.193
r_nbd_refined	0.172
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.121
r_ncsr_local_group_1	0.103
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.04
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3269
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	78

Software

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