4FMF | pdb_00004fmf

Crystal structure of human nectin-1 full ectodomain (D1-D3)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	293.15	1.8 M sodium formate, 0.1 M sodium citrate, pH 5.4, cryoprotectant: 15% 2R,3R-butane-di-ol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.288	α = 90
b = 106.288	β = 90
c = 334.622	γ = 120

Symmetry
Space Group	P 63

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		2010-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	3.2	40	99	0.1	14.2	6	35252	34857		-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	3.2	3.31	92.4		0.51	2.2	4

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ALP	3.2	20	34902	33089	1749	98.94	0.23408	0.23408	0.2328	0.25841	0.2375	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]
3.31	1.66		3.31		-4.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.769
r_dihedral_angle_4_deg	20.258
r_dihedral_angle_3_deg	18.911
r_dihedral_angle_1_deg	8.159
r_angle_other_deg	2.603
r_angle_refined_deg	1.65
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9470
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	124

Software

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