☰ Navigation Tabs
Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 16% PEG 4000 and 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.95 58.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.439 α = 90 b = 108.179 β = 90.9 c = 55.65 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 PIXEL DECTRIS PILATUS3 6M 2018-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.92 55.64 98.8 0.078 0.973 8 2.6 49393
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 1.92 1.97 98 0.305 0.788 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.92 55.493 49365 2478 98.712 0.182 0.1805 0.1877 0.2119 0.2198 22.18
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] 0.081 -0.018 0.655 -0.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.276 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_4_deg 7.308 r_lrange_it 6.009 r_dihedral_angle_1_deg 5.962 r_lrange_other 5.912 r_scangle_other 4.663 r_scangle_it 4.661 r_scbond_it 2.969 r_scbond_other 2.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.276 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_4_deg 7.308 r_lrange_it 6.009 r_dihedral_angle_1_deg 5.962 r_lrange_other 5.912 r_scangle_other 4.663 r_scangle_it 4.661 r_scbond_it 2.969 r_scbond_other 2.953 r_mcangle_other 2.872 r_mcangle_it 2.871 r_mcbond_it 1.871 r_mcbond_other 1.866 r_angle_refined_deg 1.566 r_angle_other_deg 1.366 r_nbd_refined 0.222 r_nbd_other 0.2 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.131 r_metal_ion_refined 0.114 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3354 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 71
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC phasing REFMAC refinement