2VSC

Structure of the immunoglobulin-superfamily ectodomain of human CD47


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5200 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 coefficientSolvent content
2.652.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.137α = 90
b = 47.502β = 99.31
c = 56.811γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.928.398.80.0713.93.741496-324.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9291.80.42.93.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JJS, CHAIN C1.928.1939392210098.60.2190.2160.263RANDOM25.59
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]
0.070.15-0.760.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.938
r_dihedral_angle_4_deg14.853
r_dihedral_angle_3_deg13.381
r_dihedral_angle_1_deg6.621
r_scangle_it2.133
r_scbond_it1.411
r_angle_refined_deg1.367
r_angle_other_deg0.847
r_mcangle_it0.769
r_mcbond_it0.621
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.938
r_dihedral_angle_4_deg14.853
r_dihedral_angle_3_deg13.381
r_dihedral_angle_1_deg6.621
r_scangle_it2.133
r_scbond_it1.411
r_angle_refined_deg1.367
r_angle_other_deg0.847
r_mcangle_it0.769
r_mcbond_it0.621
r_symmetry_vdw_other0.2
r_nbd_other0.196
r_nbd_refined0.181
r_nbtor_refined0.176
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.136
r_nbtor_other0.108
r_chiral_restr0.08
r_bond_refined_d0.01
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3647
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing