2VSC

Structure of the immunoglobulin-superfamily ectodomain of human CD47

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JJS	PDB ENTRY 2JJS, CHAIN C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		200 NL 17 MG/ML CD47 PLUS 100 NL RESERVOIR (0.2 M MGCL2, 0.1 M BIS-TRIS PH 5.5, 25% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 20.5 C.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.137	α = 90
b = 47.502	β = 99.31
c = 56.811	γ = 90

Symmetry
Space Group	C 1 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	MARRESEARCH	MIRRORS	2006-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.9	28.3	98.8	0.07	13.9	3.7		41496		-3	24.9

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	1.9	2	91.8		0.4	2.9	3.1

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 2JJS, CHAIN C	1.9	28.19	39392	2100	98.6	0.219	0.216	0.263	RANDOM	25.59

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]
0.07		0.15	-0.76		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.938
r_dihedral_angle_4_deg	14.853
r_dihedral_angle_3_deg	13.381
r_dihedral_angle_1_deg	6.621
r_scangle_it	2.133
r_scbond_it	1.411
r_angle_refined_deg	1.367
r_angle_other_deg	0.847
r_mcangle_it	0.769
r_mcbond_it	0.621
r_symmetry_vdw_other	0.2
r_nbd_other	0.196
r_nbd_refined	0.181
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.136
r_nbtor_other	0.108
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	3647
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	170

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing