5VNZ | pdb_00005vnz

Structure of a TRAF6-Ubc13~Ub complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HCT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		289	0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.36	α = 90
b = 170.551	β = 90
c = 97.312	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315r		2016-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3.41	107.45	99.6	0.128	0.139	0.052	0.997	9.7	7.1		16046

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.41	3.68	98.3		1.545	1.665	0.615	0.64		7.1

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	3HCT	3.41	107.45	15243	788	99.53	0.2395	0.2369	0.2365	0.2944	0.2898	RANDOM	155.826

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]
7.08			1.58		-8.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.03
r_dihedral_angle_3_deg	14.032
r_dihedral_angle_4_deg	13.067
r_dihedral_angle_1_deg	5.93
r_angle_refined_deg	1.086
r_angle_other_deg	0.859
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	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	5321
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	6

Software

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