2JJS | pdb_00002jjs

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	2UV3	PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC FOR CHAINS C AND D
experimental model	PDB	2ICC	PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC FOR CHAINS C AND D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4	278	100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.2 M POTASSIUM IODIDE, 20% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C., pH 7.4

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.477	α = 90
b = 72.41	β = 95.01
c = 89.826	γ = 90

Symmetry
Space Group	P 1 21 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	2007-04-15	M	SINGLE WAVELENGTH
2	1	x-ray

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2
2	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	1.85	29.8	100	0.14	17.6	10.3		46373		-3	19.5

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	1.85	1.92	100		0.79	2.8	9.2

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	PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC FOR CHAINS C AND D	1.85	89.44	43948	2345	99.8	0.171	0.169	0.18	0.213	0.22	RANDOM	20.2

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]
0.5		-0.09	0.34		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.176
r_dihedral_angle_4_deg	19.291
r_dihedral_angle_3_deg	10.867
r_dihedral_angle_1_deg	6.715
r_scangle_it	6.381
r_scbond_it	3.961
r_mcangle_it	2.47
r_mcbond_it	1.708
r_angle_refined_deg	1.269
r_angle_other_deg	0.842
r_symmetry_vdw_other	0.222
r_nbd_other	0.194
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.184
r_nbtor_refined	0.168
r_symmetry_hbond_refined	0.132
r_xyhbond_nbd_refined	0.127
r_nbtor_other	0.098
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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	3626
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing