4JUY | pdb_00004juy

Crystal structure of the PUB domain of E3 ubiquitin ligase RNF31

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.8M K/Na tartrate tetrahydrate, 0.5% PEG MME 5000, 0.1 M BisTris, pH 8.5, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 256.488	α = 90
b = 256.488	β = 90
c = 256.488	γ = 90

Symmetry
Space Group	F 4 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	CCD	ADSC QUANTUM 315r		2013-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97926	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	50	100	0.072	0.072	43.6	14.2	28765	28765			52.1

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	2.4	2.44	100		0.973	3	14.5	1403

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.4	49.41	28765	27821	932	99.87	0.237	0.2363	0.2422	0.2582	0.2624	RANDOM	70.9644

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.633
r_dihedral_angle_4_deg	17.108
r_dihedral_angle_3_deg	13.974
r_dihedral_angle_1_deg	5.19
r_mcangle_it	1.714
r_angle_refined_deg	1.256
r_mcbond_it	1.057
r_mcbond_other	1.056
r_angle_other_deg	0.769
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2899
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling