☰ Navigation Tabs
The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M AMMONIUM FLORIDE, 20% PEG 3350, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.89 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.32 α = 77.41 b = 76.76 β = 73.35 c = 89.41 γ = 63.57
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 ADSC CCD TOROIDAL MIRRORS 2003-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 20 97.2 0.099 17.6 3.5 108424 28.5
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 2 2.07 90.9 0.801 1.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 20 107917 5440 96.7 0.206 0.206 0.27 0.2572 RANDOM
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 Key Refinement Restraint Deviation x_dihedral_angle_d 28.8 x_scangle_it 9.5 x_scbond_it 7 x_mcangle_it 6.3 x_mcbond_it 4.3 x_angle_deg 1.4 x_improper_angle_d 0.68 x_bond_d 0.007 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 28.8 x_scangle_it 9.5 x_scbond_it 7 x_mcangle_it 6.3 x_mcbond_it 4.3 x_angle_deg 1.4 x_improper_angle_d 0.68 x_bond_d 0.007 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 Atoms Number Protein Atoms 9828 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling SHELX phasing