4FMK | pdb_00004fmk

Crystal structure of mouse nectin-2 extracellular fragment D1-D2

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	6	293.15	6% w/v PEG6000, 0.05 M cadmium sulfate, 0.2 M sodium acetate, 0.1 M MES, pH 6.0, cryoprotectant: 15% 2R,3R-butane-di-ol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
4.36	71.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.666	α = 90
b = 68.666	β = 90
c = 159.605	γ = 120

Symmetry
Space Group	P 31 1 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	CCD	MAR CCD 165 mm		2011-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9792	NSLS	X4C

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	2.54	40	99.4	0.06	20.5	6.1	14118	14118		-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	2.54	2.63	99.4		0.54	3.9	6.2

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ALP	2.56	20	14118	14118	708	99.5	0.22332	0.22332	0.22117	0.2243	0.26755	0.2717	RANDOM	88.031

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]
4.63	2.32		4.63		-6.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.712
r_dihedral_angle_4_deg	18.521
r_dihedral_angle_3_deg	17.677
r_dihedral_angle_1_deg	6.311
r_angle_refined_deg	1.667
r_angle_other_deg	1.094
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1717
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	135

Software

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