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Crystal structure of the effector domain of human Plexin B1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 291 2.6M Sodium chloride, 18% Ethylene glycol, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.979 α = 90 b = 56.571 β = 90 c = 99.366 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 2007-06-10 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2007-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97918 APS 23-ID-B 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2 50 94.8 0.067 12.2 6.4 19206
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 2.07 62.5 0.435 2.7 1248
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 20 19071 842 95.16 0.224 0.224 0.222 0.269 0.2762 thin shells 30.328
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] 1.5 -0.58 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 15.163 r_dihedral_angle_3_deg 11.63 r_dihedral_angle_1_deg 6.685 r_scangle_it 2.942 r_scbond_it 2.042 r_angle_refined_deg 1.412 r_mcangle_it 1.323 r_mcbond_it 1.03 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.288 r_dihedral_angle_4_deg 15.163 r_dihedral_angle_3_deg 11.63 r_dihedral_angle_1_deg 6.685 r_scangle_it 2.942 r_scbond_it 2.042 r_angle_refined_deg 1.412 r_mcangle_it 1.323 r_mcbond_it 1.03 r_angle_other_deg 0.926 r_nbd_refined 0.202 r_mcbond_other 0.201 r_nbd_other 0.189 r_symmetry_vdw_other 0.176 r_nbtor_refined 0.161 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.133 r_nbtor_other 0.086 r_chiral_restr 0.083 r_symmetry_hbond_refined 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1509 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection