3WXE | pdb_00003wxe

Crystal structure of CYLD USP domain (C596S) 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	50mM Tris-HCl buffer, 9% PEG4000, 100mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.676	α = 90
b = 49.788	β = 102.69
c = 71.003	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	CCD	RAYONIX MX225HE	mirrors	2013-04-20	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	2.5	50	96.9	0.094			15549	15549

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	2.5	2.54	92.4		0.329	2.9

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	2.5	50	15549	14287	766	96.97	0.18518	0.18191	0.19	0.24722	0.25	RANDOM	50.063

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		0.45	-1.2		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.27
r_dihedral_angle_4_deg	18.156
r_dihedral_angle_3_deg	17.828
r_long_range_B_refined	9.021
r_long_range_B_other	9.015
r_scangle_other	6.439
r_dihedral_angle_1_deg	6.02
r_mcangle_it	5.364
r_mcangle_other	5.363
r_scbond_it	4.264
r_scbond_other	4.263
r_mcbond_it	3.306
r_mcbond_other	3.305
r_angle_refined_deg	1.6
r_angle_other_deg	0.855
r_chiral_restr	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3617
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms

Software

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