8T2D

Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.511	α = 90
b = 46.855	β = 90
c = 91.122	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		2023-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97939	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.751	29.85	98.89	0.06022	0.0653	0.02474	0.999	12.41	6.6		17557			33.26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.751	1.813	94.24		0.9374	0.386		3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.751	29.85	17497	843	98.915	0.225	0.2224	0.2725	43.643

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]
0.232			-0.488		0.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.266
r_dihedral_angle_6_deg	14.709
r_lrange_other	7.844
r_lrange_it	7.841
r_dihedral_angle_1_deg	7.225
r_scangle_it	6.024
r_scangle_other	6.021
r_dihedral_angle_2_deg	5.676
r_mcangle_other	4.256
r_mcangle_it	4.25
r_scbond_other	3.837
r_scbond_it	3.836
r_mcbond_it	2.93
r_mcbond_other	2.929
r_angle_refined_deg	1.348
r_angle_other_deg	0.452
r_nbd_other	0.23
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.217
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1535
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
SCALA	data scaling
PHASER	phasing
XDS	data reduction