3OKY

Plexin A2 in complex with Semaphorin 6A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62932-Methyl-2,4-Pentanediol 12.4% v/v, MES 124mM pH 6.0, ethyl acetate 1% v/v, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0960.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.544α = 90
b = 159.596β = 90
c = 139.256γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1955594.48838682704-3-3

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.19539.8991.338838682680419793.610.19160.19160.18960.23
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]
13.7873-4.8816-8.9057
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.139
f_angle_d0.919
f_chiral_restr0.062
f_bond_d0.005
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9069
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms142

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling