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Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepIII-HepII-HepI 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 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.24 α = 90 b = 107.56 β = 90.84 c = 55.56 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 1.63 55.55 98.8 0.051 0.978 9.9 2.6 79745
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 1.63 1.66 98.2 0.345 0.752 2.9
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 1.63 55.295 79704 4242 98.758 0.178 0.1765 0.185 0.1991 0.208 21.667
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] 0.024 -0.023 -0.03 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_4_deg 11.854 r_dihedral_angle_1_deg 5.878 r_lrange_it 5.876 r_lrange_other 5.736 r_scangle_it 4.726 r_scangle_other 4.725 r_scbond_it 3.068 r_scbond_other 3.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_3_deg 13.335 r_dihedral_angle_4_deg 11.854 r_dihedral_angle_1_deg 5.878 r_lrange_it 5.876 r_lrange_other 5.736 r_scangle_it 4.726 r_scangle_other 4.725 r_scbond_it 3.068 r_scbond_other 3.067 r_mcangle_other 2.79 r_mcangle_it 2.789 r_mcbond_it 1.907 r_mcbond_other 1.903 r_angle_refined_deg 1.661 r_angle_other_deg 1.47 r_nbd_refined 0.226 r_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.183 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.08 r_metal_ion_refined 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3374 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 78
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC phasing REFMAC refinement