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Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKT 3OKT, 1Q47, 4GZ9 experimental model PDB 1Q47 3OKT, 1Q47, 4GZ9 experimental model PDB 4GZ9 3OKT, 1Q47, 4GZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 7.5 293 70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K 3 VAPOR DIFFUSION, SITTING DROP 7.5 293 70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.632 α = 90 b = 293.604 β = 106.38 c = 252.176 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 2M 2011-04-15 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-04-20 M SINGLE WAVELENGTH 3 3 x-ray 100 CCD ADSC QUANTUM 315r 2011-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1 2 SYNCHROTRON DIAMOND BEAMLINE I03 1.07190 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2,3 7 126 95.6 20190 20176 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3OKT, 1Q47, 4GZ9 7 125.506 -3 20176 20176 1009 95.6 0.2847 0.2847 0.281 0.2848 0.2857 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] 84.1244 119.0039 17.4558 22.6768
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.074 f_angle_d 1.202 f_chiral_restr 0.063 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35654 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose GDA data collection PHASER phasing PHENIX refinement MOSFLM data reduction Aimless data scaling