4UF6 | pdb_00004uf6

UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		STRUCTURE OF THE UCH-L5-UBIQUITIN FROM THE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			277	100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.084	α = 90
b = 137.788	β = 102.54
c = 98.916	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 2M-F		2014-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	3.69	47.74	97	0.2	5.8	4.2		21090		1.8

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	3.69	3.98	90.3		0.66	1.8	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	STRUCTURE OF THE UCH-L5-UBIQUITIN FROM THE	3.69	100.99	20030	1059	97.9	0.23956	0.238	0.2402	0.26907	0.2667	RANDOM	87.548

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]
-2.75		2.63	-1.53		2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.246
r_dihedral_angle_4_deg	18.082
r_dihedral_angle_3_deg	15.9
r_dihedral_angle_1_deg	6.626
r_angle_refined_deg	1.148
r_angle_other_deg	0.891
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13486
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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