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Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E/K203D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 The crystals were grown in hanging drops with 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as the reservoir. Before freezing for x-ray data collection, crystals were 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
Crystal Properties Matthews coefficient Solvent content 3.64 66.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.19 α = 90 b = 97.19 β = 90 c = 44.629 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 2012-10-10 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 2.3 15 99.9 0.069 18.3 5.6 10829 37.92
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 2.3 2.38 99.9 0.465 4.8 1089
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 3pak 2.301 14.649 10619 1075 97.94 0.1689 0.1652 0.1658 0.2003 0.1976 49.1631
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 16.24 f_angle_d 0.759 f_chiral_restr 0.029 f_bond_d 0.013 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1143 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction