3NY2 | pdb_00003ny2

Structure of the ubr-box of UBR2 ubiquitin ligase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.96M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.39	α = 65.05
b = 61.456	β = 89.98
c = 72.806	γ = 90.01

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 210		2010-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9779	CHESS	A1

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	2.6	50	94.8			13189	12503	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)
	2.6	2.64	79.1

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	2.61	50	1	13189	12503	652	94.36	0.24	0.23265	0.22974	0.2281	0.28808	0.284	RANDOM	32.62

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]
-4.26	0.7	-0.06	5.11	1.4	-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.287
r_dihedral_angle_4_deg	21.795
r_dihedral_angle_3_deg	17.754
r_dihedral_angle_1_deg	5.475
r_scangle_it	1.292
r_angle_refined_deg	1.094
r_scbond_it	0.768
r_mcangle_it	0.605
r_mcbond_it	0.338
r_nbtor_refined	0.295
r_symmetry_vdw_refined	0.238
r_symmetry_hbond_refined	0.2
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.083
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4297
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	24

Software

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