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Crystal structure of CD9 large extracellular loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 pentaerythritol propoxylate, potassium chloride, sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.986 α = 80.39 b = 39.998 β = 76.29 c = 63.643 γ = 68.15
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 EIGER X 16M 2019-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 29.017 95.613 0.101 0.121 0.065 0.991 4.82 3.407 22863
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 93.003 1.145 1.364 0.732 0.322 0.82 3.355
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 6RLO 2 29.017 21714 1148 95.51 0.241 0.2391 0.2441 0.2794 0.2793 RANDOM 38.814
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] -0.97 1.27 -0.32 -0.18 -0.66 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_3_deg 16.658 r_dihedral_angle_1_deg 7.429 r_dihedral_angle_4_deg 3.595 r_angle_refined_deg 1.393 r_angle_other_deg 1.309 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.513 r_dihedral_angle_3_deg 16.658 r_dihedral_angle_1_deg 7.429 r_dihedral_angle_4_deg 3.595 r_angle_refined_deg 1.393 r_angle_other_deg 1.309 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2525 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose EVAL15 data reduction EVAL15 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction