3WXF | pdb_00003wxf

Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VHF	PDB entry 2VHF and 1UBQ
experimental model	PDB	1UBQ	PDB entry 2VHF and 1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.628	α = 77.66
b = 65.372	β = 89.04
c = 69.846	γ = 89.46

Symmetry
Space Group	P 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	CCD	RAYONIX MX225HE	mirrors	2013-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	50	97.6	0.095			38724	38724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	95.4		0.41	2.41

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2VHF and 1UBQ	2.3	49.62	38724	35341	1874	97.63	0.1892	0.1871	0.1911	0.2285	0.2278	RANDOM	37.948

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]
0.43	-0.1	0.15	-0.81	0.28	0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.509
r_dihedral_angle_4_deg	23.167
r_dihedral_angle_3_deg	20.118
r_dihedral_angle_1_deg	6.635
r_mcangle_it	3.655
r_mcbond_it	2.231
r_mcbond_other	2.23
r_angle_refined_deg	1.729
r_angle_other_deg	1.135
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7201
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling