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X-ray structure of human Dscam Ig7-Ig9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 292 Glycerol, calcium acetate, PEG 8000, HEPES
Crystal Properties Matthews coefficient Solvent content 3.48 64.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.599 α = 90 b = 71.421 β = 113.061 c = 92.174 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 6M 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 84.81 99 0.044 0.051 0.026 1 12.8 3.8 39662 36.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 97.4 0.874 1.011 0.501 0.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4wvr 1.85 84.808 39659 2001 98.782 0.196 0.1947 0.2003 0.228 0.2352 56.811
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] -1.329 1.17 0.428 -0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.117 r_dihedral_angle_4_deg 15.353 r_dihedral_angle_3_deg 13.846 r_lrange_it 11.9 r_lrange_other 11.898 r_scangle_it 9.867 r_scangle_other 9.865 r_dihedral_angle_1_deg 7.64 r_mcangle_it 7.219 r_mcangle_other 7.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.117 r_dihedral_angle_4_deg 15.353 r_dihedral_angle_3_deg 13.846 r_lrange_it 11.9 r_lrange_other 11.898 r_scangle_it 9.867 r_scangle_other 9.865 r_dihedral_angle_1_deg 7.64 r_mcangle_it 7.219 r_mcangle_other 7.217 r_scbond_it 6.844 r_scbond_other 6.841 r_mcbond_other 5.483 r_mcbond_it 5.482 r_angle_refined_deg 1.85 r_angle_other_deg 1.321 r_symmetry_nbd_refined 0.248 r_nbd_other 0.207 r_symmetry_nbd_other 0.197 r_nbd_refined 0.193 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_symmetry_metal_ion_refined 0.042 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing