1OLZ

The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2 M AMMONIUM FLORIDE, 20% PEG 3350, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.8957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.32α = 77.41
b = 76.76β = 73.35
c = 89.41γ = 63.57
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRRORS2003-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
122097.20.09917.63.510842428.5
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)
122.0790.90.8011.83

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT220107917544096.70.2060.2060.27RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.8
x_scangle_it9.5
x_scbond_it7
x_mcangle_it6.3
x_mcbond_it4.3
x_angle_deg1.4
x_improper_angle_d0.68
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.8
x_scangle_it9.5
x_scbond_it7
x_mcangle_it6.3
x_mcbond_it4.3
x_angle_deg1.4
x_improper_angle_d0.68
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9828
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms

Software

Software
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing