8XPN | pdb_00008xpn

The Crystal Structure of USP8 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.83	α = 90
b = 109.342	β = 90
c = 180.992	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 EIGER X 9M		2023-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95355	CLSI	08ID-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	2.1	48.777	99.5	0.149	11.7	9		67580

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	2.1	2.15			0.973

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	2.1	48.777	67509	3285	99.383	0.178	0.1765	0.19	0.216	0.22	35.216

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]
-0.838			0.379		0.459

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.274
r_dihedral_angle_other_3_deg	13.09
r_dihedral_angle_3_deg	12.258
r_lrange_it	6.868
r_lrange_other	6.853
r_dihedral_angle_1_deg	6.36
r_dihedral_angle_2_deg	5.046
r_scangle_it	4.912
r_scangle_other	4.912
r_mcangle_it	3.78
r_mcangle_other	3.78
r_scbond_it	3.013
r_scbond_other	3.013
r_mcbond_it	2.395
r_mcbond_other	2.393
r_angle_refined_deg	1.25
r_angle_other_deg	0.449
r_nbd_other	0.22
r_nbd_refined	0.206
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.138
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.066
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8197
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	18

Software

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