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N-terminal domain of mouse surfactant protein B with bound lipid, Y59A/H79A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VYN 6VYN, lipid removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293.15 100 mM Na/K phosphate pH 6.2, 200 mM NaCl, 47.5% (w/v) PEG 200
Crystal Properties Matthews coefficient Solvent content 2.88 57.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.335 α = 90 b = 169.527 β = 126.897 c = 73.714 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-F 2018-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
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 2.31 84.76 97.45 0.08439 0.995 13.34 6.9 37983 77.25
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 2.31 2.397 80.13 2.03 0.518 0.72 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VYN, lipid removed 2.31 84.76 0.32 37542 1826 97.45 0.2422 0.2411 0.2469 0.2619 0.2693 106.28
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.683 f_angle_d 0.6725 f_chiral_restr 0.0376 f_plane_restr 0.0041 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4992 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 603
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building