4FQP | pdb_00004fqp

Crystal structure of human Nectin-like 5 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	3EOW	PDB ENTRY 3EOW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293.15	55% v/v tacsimate, 0.1 M Bicine, pH 9.0, with additional 10% tacsimate as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
11.12	88.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.919	α = 90
b = 138.919	β = 90
c = 273.645	γ = 120

Symmetry
Space Group	P 65 2 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		2011-06-30	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	3.563	40	99.8	0.11	13.7	6.3	19387	19387

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	3.563	3.73	99.9		0.55	2.5	5.7

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 3EOW	3.6	20	19387	17687	963	98.82	0.24953	0.24953	0.24831	0.2513	0.27248	0.2838	RANDOM	116.427

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]
6.81	3.4		6.81		-10.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.044
r_dihedral_angle_3_deg	20.406
r_dihedral_angle_4_deg	13.525
r_dihedral_angle_1_deg	7.599
r_angle_other_deg	3.064
r_angle_refined_deg	1.761
r_chiral_restr	0.403
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2342
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	257

Software

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