2VC2

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TXV	PDB ENTRY 1TXV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10-12% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.151	α = 90
b = 149.151	β = 90
c = 176.217	γ = 120

Symmetry
Space Group	P 32 2 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 CCD	MIRROR	2003-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1

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	3.1	50	99.9	0.14	12.1	7		41563

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	3.1	3.2	99.7		0.56	2.7	6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TXV	3.1	42.72	38636	2044	97.7	0.179	0.177	0.217	RANDOM	3.21

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]
1.04	0.52		1.04		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.205
r_dihedral_angle_4_deg	14.475
r_dihedral_angle_3_deg	13.057
r_dihedral_angle_1_deg	5.376
r_scangle_it	1.692
r_mcangle_it	1.274
r_angle_refined_deg	1.001
r_scbond_it	0.955
r_mcbond_it	0.826
r_angle_other_deg	0.765
r_nbd_refined	0.184
r_nbd_other	0.173
r_nbtor_refined	0.173
r_symmetry_vdw_other	0.147
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.113
r_symmetry_hbond_refined	0.11
r_symmetry_vdw_refined	0.103
r_mcbond_other	0.1
r_nbtor_other	0.081
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_xyhbond_nbd_other	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10297
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	240

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing