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Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic PhosII-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 2.87 57.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.13 α = 90 b = 106.25 β = 91.13 c = 55.34 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 1.85 53.13 98.8 0.061 0.99 9.2 2.5 53663
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 1.85 1.89 98.9 0.333 0.674 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 1.85 49.122 53633 2770 98.746 0.18 0.1784 0.1876 0.2008 0.2053 24.891
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] 0.023 -0.16 1.083 -1.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.377 r_dihedral_angle_4_deg 17.236 r_dihedral_angle_3_deg 14.72 r_lrange_it 7.054 r_lrange_other 6.992 r_dihedral_angle_1_deg 5.822 r_scangle_it 5.738 r_scangle_other 5.737 r_scbond_it 3.613 r_scbond_other 3.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.377 r_dihedral_angle_4_deg 17.236 r_dihedral_angle_3_deg 14.72 r_lrange_it 7.054 r_lrange_other 6.992 r_dihedral_angle_1_deg 5.822 r_scangle_it 5.738 r_scangle_other 5.737 r_scbond_it 3.613 r_scbond_other 3.613 r_mcangle_other 3.193 r_mcangle_it 3.191 r_mcbond_it 2.235 r_mcbond_other 2.23 r_angle_refined_deg 1.64 r_angle_other_deg 1.43 r_nbd_other 0.227 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.135 r_metal_ion_refined 0.107 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_symmetry_metal_ion_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 3441 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 69
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC phasing REFMAC refinement