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Drosophila Plexin A in complex with Semaphorin 1b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKY 3OKY, 6FKK experimental model PDB 6FKK 3OKY, 6FKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M HEPES (pH 7.0) and 8% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.86 68.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.94 α = 90 b = 195.09 β = 90 c = 124.84 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2016-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.072 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.96 76.864 93.78 0.174 0.99 8.86 4.6 31584 69.89
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 2.96 3.07 0.634
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OKY, 6FKK 2.96 76.864 1.34 31582 1515 93.79 0.1891 0.1862 0.1855 0.2462 0.2453
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 f_dihedral_angle_d 9.797 f_angle_d 0.755 f_chiral_restr 0.048 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7941 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 178
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing