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Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E/K203D) Complexed with Mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WR9 PDB entry 4WR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 The crystal was grown in hanging drops using 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as a reservoir. Before freezing for x-ray data collection, crystal was soaked in reservoir solution of 10 mM calcium acetate without glycerol, but with stepwise additions of 5, 10, and 15% 2-methyl-2,4-pentanediol with 25% mannose for 10 minutes at each step
Crystal Properties Matthews coefficient Solvent content 3.65 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.944 α = 90 b = 96.944 β = 90 c = 44.994 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2012-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 15 98.5 0.052 23.8 5.2 18934 35.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 99.8 0.507 4.6 1893
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 FOURIER SYNTHESIS FREE R-VALUE PDB entry 4WR9 1.9 14.963 1.35 18923 1906 98.52 0.1754 0.1723 0.1774 0.2022 0.203 45.49
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 14.292 f_angle_d 1.539 f_chiral_restr 0.06 f_bond_d 0.02 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1120 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction