5OU9 | pdb_00005ou9

Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.1 M MMT-buffer pH 9.0 25% (w/v) PEG1500

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.72	α = 90
b = 59.72	β = 90
c = 319.72	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 315r		2013-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.5	79.93	99.9	0.113	0.984	8.5	6.4		21273			56.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.61	100		0.971	0.646		6.8

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	5OU7	2.5	79.93	20113	1064	99.85	0.22955	0.22791	0.23	0.26027	0.26	RANDOM	69.524

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]
-0.69			-0.69		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.908
r_dihedral_angle_4_deg	16.262
r_dihedral_angle_3_deg	16.25
r_dihedral_angle_1_deg	7.283
r_long_range_B_refined	4.149
r_long_range_B_other	4.105
r_mcangle_it	2.765
r_mcangle_other	2.765
r_scangle_other	1.951
r_angle_refined_deg	1.564
r_mcbond_it	1.495
r_mcbond_other	1.495
r_angle_other_deg	1.157
r_scbond_it	1.043
r_scbond_other	1.043
r_chiral_restr	0.127
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3088
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing