Experiment: 3X0E

Crystal structure of the ectodomain of human CD81 large extracellular loop (hCD81-LEL)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BKH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.2M Magnesium acetate 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.124	α = 90
b = 77.408	β = 107.94
c = 38.497	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r	mirrors	2013-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.834	36.625	97	0.016	16.63	6.6	15251	14801	-3	-3	31.502

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.94	86.1		0.515	5	5.56	2451

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	4BKH	1.844	29.61	1.38	15251	14771	737	98.59	0.1965	0.195	0.1933	0.225	0.2234	RANDOM	33.266

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]
-0.8642		5.9985	-6.3708		7.235

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.117
f_angle_d	0.901
f_chiral_restr	0.054
f_bond_d	0.007
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1350
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	5

Software

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