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Surfactant Protein-A neck and carbohydrate recognition domain (NCRD) in the absence of ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R13 PDB CODE 1R13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 1 ul of SP-A (10 mg/ml) was mixed with 1 ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, and 10 mM calcium chloride). After crystals had grown, the drop was diluted 1/2 with 50 mM sodium cacodylate (pH = 6.5) and 10 mM calcium chloride. Maltose powder was then added to the drop and dissolved. Prior to data collection, the drop was diluted 1/2 again and more maltose powder was dissolved., VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.75 67.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.351 α = 90 b = 98.351 β = 90 c = 44.744 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 90 IMAGE PLATE RIGAKU RAXIS IV 2006-07-07 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 50 98.2 0.039 21.9 4 10984 -3 44
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) 2.3 2.35 91.3 0.266 4.3 2.9 683
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 FOURIER SYNTHESIS THROUGHOUT PDB CODE 1R13 2.3 32.19 10788 867 96.4 0.227 0.227 0.2226 0.238 0.2366 RANDOM 45.3
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] 5.85 9.05 5.85 -11.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.2 c_improper_angle_d 0.69 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.2 c_improper_angle_d 0.69 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1135 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 11
Software Software Software Name Purpose CrystalClear data collection CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing