7NMU

Crystal structure of human platelet glycoprotein VI in complex with an inhibitory nanobody.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283.15	0.2 M calcium acetate, 0.1M sodium cacodylate pH 6.5, 18% PEG8K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.906	α = 90
b = 84.751	β = 90
c = 124.041	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	283.15	PIXEL	DECTRIS PILATUS3 6M		2019-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96864	Diamond	I24

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	2.498	84.75	98.6	0.122	0.991	8.67	6.3		26173

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56			0.834

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2gi7	2.5	70.08	26173	1329	99.893	0.177	0.1742	0.2351	40.536

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]
0.818			-0.839		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.892
r_dihedral_angle_4_deg	18.373
r_dihedral_angle_3_deg	16.113
r_dihedral_angle_1_deg	8.728
r_lrange_other	8.546
r_lrange_it	8.543
r_scangle_it	5.954
r_scangle_other	5.953
r_mcangle_it	5.236
r_mcangle_other	5.235
r_scbond_it	3.784
r_scbond_other	3.783
r_mcbond_other	3.369
r_mcbond_it	3.368
r_angle_refined_deg	1.551
r_angle_other_deg	1.211
r_metal_ion_refined	0.197
r_symmetry_nbd_other	0.191
r_nbd_refined	0.186
r_symmetry_nbd_refined	0.181
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.065
r_symmetry_metal_ion_refined	0.028
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4664
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
BUCCANEER	model building
PHASER	phasing
xia2	data scaling