2NSQ | pdb_00002nsq

Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TJM	PDB ENTRY 1TJM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	298	14% PEG 4000, 0.2 M NaOAc, pH 6.5, 1 mM DTT. 20% Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.93	α = 90
b = 60.036	β = 90
c = 74.51	γ = 90

Symmetry
Space Group	P 21 21 21

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++		2006-10-16	M	SINGLE WAVELENGTH

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

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	1.85	30	98.1	0.081	23.07	7.1		12925		-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	1.85	1.92	88.1		0.638	2	3

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 1TJM	1.85	27.84	12893	12260	631	98.1	0.174	0.171	0.18	0.218	0.23	RANDOM	21.92

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]
1.59			-0.82		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.697
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_4_deg	13.932
r_dihedral_angle_1_deg	6.842
r_scangle_it	5.292
r_scbond_it	3.873
r_mcangle_it	2.818
r_mcbond_it	2.057
r_angle_refined_deg	1.699
r_nbtor_refined	0.314
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.197
r_xyhbond_nbd_refined	0.162
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.137
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1139
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	10

Software

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