2JJT

Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JJS	PDB ENTRY 2JJS CHAINS A AND C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	278	100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.1 M CITRATE PH 5.0, 30% W/V PEG 3000) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C.

Crystal Properties
Matthews coefficient	Solvent content
2.07	33.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.62	α = 90
b = 63.72	β = 90
c = 123.02	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	100	CCD	MARRESEARCH	MIRRORS	2006-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.3	40	99.5	0.19	7.4	7		19339		-3	31.2

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	2.3	2.45	98.5		0.57	3.9	6.7

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 CHAINS A AND C	2.3	26.81	18293	989	99.5	0.238	0.235	0.288	RANDOM	24.7

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]
-2.62			4.4		-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.081
r_dihedral_angle_4_deg	14.203
r_dihedral_angle_3_deg	12.749
r_dihedral_angle_1_deg	6.564
r_scangle_it	1.266
r_angle_refined_deg	1.193
r_scbond_it	0.842
r_angle_other_deg	0.821
r_mcangle_it	0.465
r_mcbond_it	0.322
r_symmetry_vdw_other	0.276
r_nbd_other	0.194
r_nbtor_refined	0.17
r_nbd_refined	0.168
r_xyhbond_nbd_refined	0.155
r_symmetry_vdw_refined	0.133
r_symmetry_hbond_refined	0.126
r_nbtor_other	0.091
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_bond_other_d	0.004
r_gen_planes_refined	0.003
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	3506
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing