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Mouse Semaphorin 6A extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OLZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 22-24% (wt/vol) PEG 1500, 0.1M Tris-Cl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.474 α = 90 b = 89.06 β = 102.2 c = 95.523 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 270 2009-03-18 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 2.5 44.54 99.8 0.073 8.8 4.4 40593 -3 50.8
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) 2.5 2.64 99.2 0.389 1.9 4.3 5879
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 1OLZ 2.5 44.54 38510 2083 99.77 0.21467 0.21125 0.2091 0.27769 0.2754 RANDOM 40.23
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] 4.06 1.09 -2.08 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_4_deg 19.56 r_dihedral_angle_3_deg 15.825 r_dihedral_angle_1_deg 6.501 r_scangle_it 2.038 r_scbond_it 1.185 r_angle_refined_deg 1.18 r_mcangle_it 0.998 r_mcbond_it 0.533 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_4_deg 19.56 r_dihedral_angle_3_deg 15.825 r_dihedral_angle_1_deg 6.501 r_scangle_it 2.038 r_scbond_it 1.185 r_angle_refined_deg 1.18 r_mcangle_it 0.998 r_mcbond_it 0.533 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 8182 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 84
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling