3NY3 | pdb_00003ny3

Structure of the ubr-box of UBR2 in complex with N-degron

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.123	α = 90
b = 36.94	β = 109.6
c = 29.824	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	IMAGE PLATE	RIGAKU RAXIS IV++	osmic multilayer confocal	2010-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	50	99.2			7638	7577	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.63	85.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.6	28.09	1	7638	7577	365	98.9	0.192	0.19127	0.1904	0.1851	0.20987	0.2141	RANDOM	20.671

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]
-0.51		-0.88	-0.13		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.917
r_dihedral_angle_4_deg	28.103
r_dihedral_angle_3_deg	11.511
r_dihedral_angle_1_deg	5.558
r_scangle_it	2.303
r_scbond_it	1.762
r_angle_refined_deg	1.17
r_mcangle_it	1.088
r_mcbond_it	0.833
r_symmetry_vdw_refined	0.311
r_nbtor_refined	0.309
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.102
r_chiral_restr	0.074
r_metal_ion_refined	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	576
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	3

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling