8CMS

OTUB2 in covalent complex with LN5P45

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 %v/v 2-Propanol 13 %w/v PEG 4K 0.1 M HEPES pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.65	α = 90
b = 45.25	β = 96.05
c = 58	γ = 90

Symmetry
Space Group	P 1 21 1

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 9M		2020-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	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	1.77	47.43	99.6	0.118	0.142	0.077	0.994	7	3.2		24095

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.81	99.6		1.295	0.985	0.338	0.7	2.7

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	1.77	47.43	24082	1229	99.591	0.212	0.2099	0.2521	25.72

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]
0.805		-0.657	-0.279		-0.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.263
r_dihedral_angle_4_deg	16.98
r_dihedral_angle_3_deg	16.396
r_dihedral_angle_other_3_deg	8.61
r_dihedral_angle_1_deg	6.988
r_lrange_other	6.633
r_lrange_it	6.628
r_scangle_it	5.37
r_scangle_other	5.368
r_scbond_it	3.399
r_scbond_other	3.398
r_mcangle_it	3.186
r_mcangle_other	3.18
r_mcbond_it	2.12
r_mcbond_other	2.103
r_angle_refined_deg	1.654
r_angle_other_deg	1.408
r_symmetry_nbd_refined	0.373
r_symmetry_xyhbond_nbd_refined	0.223
r_nbd_refined	0.218
r_nbd_other	0.215
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.177
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_other	0.123
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1857
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	17

Software

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