8Y9A | pdb_00008y9a

The Crystal Structure of USP8 from Biortus.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	4.0M Na formate

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.008	α = 90
b = 103.008	β = 90
c = 93.254	γ = 120

Symmetry
Space Group	H 3 2

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 S 6M		2020-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.239850	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.1	40.24	98.7	0.119	9.6	5.5		3507

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.31			0.824

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.1	40.24	3507	166	97.824	0.201	0.1979	0.21	0.2681	0.27	87.712

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]
2.62	1.31		2.62		-8.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.725
r_dihedral_angle_3_deg	12.271
r_lrange_it	9.399
r_lrange_other	9.373
r_scangle_it	5.547
r_scangle_other	5.543
r_dihedral_angle_1_deg	5.519
r_mcangle_it	5.307
r_mcangle_other	5.307
r_mcbond_it	3.454
r_mcbond_other	3.42
r_dihedral_angle_2_deg	3.381
r_scbond_it	3.351
r_scbond_other	3.345
r_angle_refined_deg	0.749
r_angle_other_deg	0.272
r_nbd_refined	0.226
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.173
r_nbd_other	0.151
r_symmetry_nbd_refined	0.142
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.036
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1060
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

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