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Crystal Structure of Rat Surfactant Protein A neck and carbohydrate recognition domain (NCRD) complexed with Mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R13 PDB ENTRY 1R13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 1 ul 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 grew, the drop was diluted 1/2 with 50 mM sodium cacodylate (pH =6.5) and 10 mM calcium chloride. Then, mannose powder was added to the drop and mixed to dissolve. A second dilution by 1/2 again and addition of more mannose powder preceded data collection., VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.73 67.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.796 α = 90 b = 97.796 β = 90 c = 45.088 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 1.9 50 99.4 0.05 24.5 5 19500 -3 27.3
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) 1.9 1.94 98.9 0.287 4.5 3.9 1279
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 ENTRY 1R13 1.9 26.1 19155 1507 97.7 0.218 0.218 0.2066 0.243 0.2314 RANDOM 36.9
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] 4.35 2.62 4.35 -8.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_angle_deg 1.1 c_improper_angle_d 0.69 c_bond_d 0.004 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 22.2 c_angle_deg 1.1 c_improper_angle_d 0.69 c_bond_d 0.004 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 1143 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 19
Software Software Software Name Purpose CrystalClear data collection CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing