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Surfactant Protein A neck and carbohydrate recognition domain (NCRD) complexed with alpha-methylmannose
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 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 about 1/2 with 50 mM sodium cacodylate (pH = 6.5) and 10 mM calcium chloride. Alpha-methylmannose powder was added to the drop and stirred to dissolve. Prior to data collection, the drop was diluted about 1/2 again and more powdered alpha-methylmannose added., VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.69 66.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.452 α = 90 b = 97.452 β = 90 c = 44.848 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 2.1 50 99.6 0.038 21.5 4 14325 -3 24.7
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) 2.1 2.15 99.8 0.379 3.9 3.9 946
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 2.1 30.73 13931 1115 96.8 0.223 0.223 0.2218 0.244 0.2452 RANDOM 40.2
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] 2.57 2.71 2.57 -5.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_angle_deg 1.1 c_improper_angle_d 0.68 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1143 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 20
Software Software Software Name Purpose CrystalClear data collection CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing