7NLC | pdb_00007nlc

Crystallographic structure of human Tsg101 UEV domain in complex with a HEV ORF3 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	288	0.1M Citric Acid, 2M Ammonium sulfate pH 3.5, 13.34% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.57	α = 90
b = 42.57	β = 90
c = 188.16	γ = 90

Symmetry
Space Group	P 41 21 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	PIXEL	DECTRIS EIGER X 9M		2020-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980108	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.398	47.084	100	1	23.7	4.6		35532

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48			0.875

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3OBQ	1.398	47.084	35531	1777	99.952	0.221	0.2199	0.23	0.239	0.24	24.312

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]
0.244			0.244		-0.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.864
r_dihedral_angle_4_deg	23.385
r_dihedral_angle_3_deg	13.03
r_dihedral_angle_1_deg	6.282
r_angle_refined_deg	1.786
r_angle_other_deg	1.374
r_symmetry_nbd_refined	0.319
r_nbd_refined	0.23
r_nbd_other	0.227
r_nbtor_refined	0.193
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.137
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1210
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling
MOLREP	phasing