2NQ3 | pdb_00002nq3

Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FK9	PDB entry 2FK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	The protein at 20 mg/ml was dissolved in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol, 2 mM DTT, and mixed 1:1 with well solution that was 20% PEG3350, 0.1 M bis-Tris, pH 6.0, 0.2 M NH4OAc, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.499	α = 90
b = 82.499	β = 90
c = 65.273	γ = 120

Symmetry
Space Group	P 32 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	100	IMAGE PLATE	RIGAKU RAXIS IV++		2006-09-09	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)	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	1.8	25	100	0.09	29.2	10.7	24173	24173		-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)
	1.8	1.83	100		0.9	3.4	10.4	1192

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 2FK9	1.8	24.1	24145	22908	1233	99.98	0.16352	0.16194	0.17	0.19544	0.2	RANDOM	32.203

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]
0.05	0.03		0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.758
r_dihedral_angle_4_deg	29.428
r_dihedral_angle_3_deg	10.904
r_dihedral_angle_1_deg	6.688
r_scangle_it	5.91
r_scbond_it	3.75
r_mcangle_it	2.918
r_mcbond_it	2.044
r_angle_refined_deg	1.6
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.758
r_dihedral_angle_4_deg	29.428
r_dihedral_angle_3_deg	10.904
r_dihedral_angle_1_deg	6.688
r_scangle_it	5.91
r_scbond_it	3.75
r_mcangle_it	2.918
r_mcbond_it	2.044
r_angle_refined_deg	1.6
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.201
r_chiral_restr	0.138
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1063
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	1

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.