4S1Z

Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WWZ	2WWZ, 1UBQ
experimental model	PDB	1UBQ	2WWZ, 1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	285	100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.222	α = 90
b = 123.971	β = 103.68
c = 78.312	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	285	PIXEL	DECTRIS PILATUS 6M-F	COMPOUND REFRACTIVE LENSES	2014-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	76.1	99	0.072	15.64	3.5		17755		-3	85.71

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	3.1	95.3		0.4869	2.05	3.4

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	2WWZ, 1UBQ	3.03	76.1	16797	957	98.8	0.225	0.222	0.23	0.27	0.27	RANDOM	81.9

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]
8.64		0.36	3.02		-10.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.454
r_dihedral_angle_3_deg	13.457
r_dihedral_angle_4_deg	11.294
r_long_range_B_refined	5.25
r_long_range_B_other	5.249
r_dihedral_angle_1_deg	4.563
r_mcangle_it	3.254
r_mcangle_other	3.254
r_scangle_other	3.087
r_mcbond_it	1.893
r_mcbond_other	1.889
r_scbond_it	1.777
r_scbond_other	1.776
r_angle_refined_deg	0.84
r_angle_other_deg	0.69
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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	3623
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

Software
Software Name	Purpose
EDNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling