2ONI | pdb_00002oni

Catalytic Domain of the Human NEDD4-like E3 Ligase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947.

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.058	α = 90
b = 103.058	β = 90
c = 182.214	γ = 120

Symmetry
Space Group	P 63 2 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 210	mirror	2006-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97922	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	30	99.7	0.091	35.3	11	29656	29656		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	99.9		0.84	3.3	11.3	2878

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	28.28	28067	1534	99.62	0.20896	0.20632	0.2015	0.25916	0.2501	RANDOM	44.493

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]
-0.21	-0.11		-0.21		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.573
r_dihedral_angle_4_deg	16.987
r_dihedral_angle_3_deg	16.588
r_scangle_it	6.441
r_dihedral_angle_1_deg	6.255
r_scbond_it	4.779
r_mcangle_it	3.051
r_mcbond_it	1.982
r_angle_refined_deg	1.543
r_nbtor_refined	0.313
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.128
r_chiral_restr	0.123
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3121
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	1

Software

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