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Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PW9 pdbid 1PW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M Tris pH 7.0, 16% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.95 58.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.329 α = 90 b = 108.14 β = 91.82 c = 55.67 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 PILATUS 6M 2013-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 55.3 93.2 0.066 0.083 0.05 0.991 7.3 2.3 61250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 91.2 0.359 0.459 0.281 0.774 2.3
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 pdbid 1PW9 1.75 55.3 58070 3158 92.98 0.1743 0.1732 0.1826 0.1958 0.2044 RANDOM 23.556
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] -0.14 0.06 1.07 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.279 r_dihedral_angle_3_deg 11.685 r_dihedral_angle_4_deg 7.94 r_dihedral_angle_1_deg 5.472 r_angle_refined_deg 1.402 r_angle_other_deg 0.921 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.279 r_dihedral_angle_3_deg 11.685 r_dihedral_angle_4_deg 7.94 r_dihedral_angle_1_deg 5.472 r_angle_refined_deg 1.402 r_angle_other_deg 0.921 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3469 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 91
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction