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WT Ig-like V Domain with Phosphatidylserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M NaI, 1.6 M ammonium sulfate, 50 mM Tris 8.5
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.331 α = 90 b = 160.331 β = 90 c = 86.205 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 S 6M 2017-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00001 ALS 5.0.2
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 2.2 47.36 100 0.106 0.999 19.8 13.1 57469
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 1.733 0.579 13.4
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 5UD7 2.2 47.36 54638 2768 99.98 0.2236 0.2217 0.228 0.2606 0.2651 RANDOM 52.028
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] 0.21 0.21 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 18.566 r_dihedral_angle_4_deg 18.309 r_dihedral_angle_1_deg 7.456 r_angle_refined_deg 2.165 r_angle_other_deg 1.062 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 18.566 r_dihedral_angle_4_deg 18.309 r_dihedral_angle_1_deg 7.456 r_angle_refined_deg 2.165 r_angle_other_deg 1.062 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5058 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction