8OXR

Structure of the N-terminal didomain d1_d2 of the Thrombospondin type-1 domain-containing 7A

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M sodium chloride, 0.1 M bis-tris, 1.5 M ammonium sulphate, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.843	α = 90
b = 108.714	β = 90
c = 53.536	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X CdTe 16M		2020-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9762	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	57.56	99.8	1	10.8	13.2		9135

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	2.3	2.38			0.62	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	57.555	9111	475	99.792	0.23	0.227	0.2916	58.873

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]
1.122			-2.418		1.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.893
r_dihedral_angle_6_deg	13.799
r_lrange_other	13.438
r_lrange_it	13.43
r_scangle_it	11.161
r_scangle_other	11.154
r_mcangle_other	8.522
r_mcangle_it	8.495
r_dihedral_angle_1_deg	7.411
r_dihedral_angle_2_deg	7.249
r_scbond_it	7.237
r_scbond_other	7.231
r_mcbond_it	5.639
r_mcbond_other	5.622
r_angle_refined_deg	1.6
r_angle_other_deg	0.507
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.186
r_nbd_other	0.135
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_nbd_refined	0.103
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1022
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing