3NIF | pdb_00003nif

The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific Antagonist That Does Not Induce Opening

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.9	277	11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 259.53	α = 90
b = 144.28	β = 90
c = 104.35	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARMOSAIC 300 mm CCD		2008-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.00795	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	50	95.1	0.089	0.089	13.3	5.53	153422	145845

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)
	2.4	2.46	95.6		0.956	2.29	5.1	11242

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 (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	3NID	2.4	48.21	144984	860	95.07	0.17586	0.17563	0.19	0.21611	0.22	RANDOM	13.72

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]
-0.45			0.56		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.242
r_dihedral_angle_4_deg	13.598
r_dihedral_angle_3_deg	12.861
r_scangle_it	6.954
r_dihedral_angle_1_deg	5.737
r_scbond_it	4.714
r_mcangle_it	3.155
r_mcbond_it	1.775
r_angle_refined_deg	1.092
r_angle_other_deg	0.783

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.242
r_dihedral_angle_4_deg	13.598
r_dihedral_angle_3_deg	12.861
r_scangle_it	6.954
r_dihedral_angle_1_deg	5.737
r_scbond_it	4.714
r_mcangle_it	3.155
r_mcbond_it	1.775
r_angle_refined_deg	1.092
r_angle_other_deg	0.783
r_mcbond_other	0.363
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20715
Nucleic Acid Atoms
Solvent Atoms	790
Heterogen Atoms	361

Software

Software
Software Name	Purpose
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.