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Mouse Plexin A2 extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 24-28%(wt/vol) PEG 3350, 0-0.2M NaCl, 0.1M Tris-Cl pH 8.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.702 α = 109.8 b = 60.677 β = 92.47 c = 95.385 γ = 112.53
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 QUANTUM 270 2009-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 2.1 42.56 98 0.069 15.4 4.7 60889 -3 27.809
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) 2.1 2.21 97 0.289 4 4.7 8828
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1SHY 2.1 42.56 57811 3075 98.01 0.20777 0.2051 0.2039 0.25748 0.2561 RANDOM 25.626
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] -0.84 0.78 0.19 0.45 -0.92 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.547 r_dihedral_angle_4_deg 16.839 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_1_deg 6.52 r_scangle_it 2.848 r_scbond_it 1.76 r_mcangle_it 1.297 r_angle_refined_deg 1.272 r_mcbond_it 0.695 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.547 r_dihedral_angle_4_deg 16.839 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_1_deg 6.52 r_scangle_it 2.848 r_scbond_it 1.76 r_mcangle_it 1.297 r_angle_refined_deg 1.272 r_mcbond_it 0.695 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8118 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 26
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling