5C7J | pdb_00005c7j

CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant

Crystal Properties
Matthews coefficient	Solvent content
3	58.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.867	α = 90
b = 139.867	β = 90
c = 59.386	γ = 120

Symmetry
Space Group	P 32

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 315	ADSC Q315	2013-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3	50	100	0.071	0.074	0.028	8.7	7.6		26035

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	100		0.979	0.37	0.754		7.8	1286

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2ZNV	3	50.01	25473	549	99.97	0.2283	0.22724	0.23	0.27659	0.27	RANDOM	96.238

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]
-0.73	-0.37		-0.73		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_3_deg	14.784
r_dihedral_angle_4_deg	14.769
r_long_range_B_refined	8.905
r_long_range_B_other	8.905
r_mcangle_it	6.248
r_mcangle_other	6.248
r_dihedral_angle_1_deg	6.229
r_scangle_other	5.916
r_mcbond_it	3.933
r_mcbond_other	3.933
r_scbond_it	3.606
r_scbond_other	3.606
r_angle_refined_deg	1.116
r_angle_other_deg	0.937
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7127
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
PHASER	phasing