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Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/K203D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAK PDB code 3PAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 DEDN (17 mg/ml) crystallized in hanging drops from a reservoir solution of 0.2 M calcium chloride and 14% (w/v) PEG 3,350. Before freezing, crystals were soaked in reservoir solution supplemented with 1.5 M 1,6-hexanediol as a cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.774 α = 90 b = 68.774 β = 90 c = 168.852 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 2013-01-17 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 1.8 15 99.4 0.065 27.1 10.7 14534 32.26
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 1.8 1.86 99.9 0.473 9.1 1451
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB code 3PAK 1.8 13.644 14368 1431 98.27 0.2088 0.2051 0.2426 0.2744 32.45
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 14.131 f_angle_d 1.208 f_chiral_restr 0.083 f_bond_d 0.011 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1097 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction