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Surfactant Protein-A neck and carbohydrate recognition domain (NCRD) complexed with glycerol
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 1ul SP-A (10 mg/ml) was mixed with 1ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, 10 mM calcium chloride, and 5 % v/v glycerol. Prior to data collection, crystals were cryoprotected in a solution with higher amounts of glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.69 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.376 α = 90 b = 97.376 β = 90 c = 44.905 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 CCD ADSC QUANTUM 4r 2002-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9795 NSLS X8C
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 25 99.6 0.044 14.8 5 22680 -3 18
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 98.2 0.229 5.6 3 2206
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 1.8 23.39 22095 2187 97.1 0.207 0.207 0.203 0.223 0.2205 RANDOM 27.9
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] 0.92 0.35 0.92 -1.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_angle_deg 1.1 c_improper_angle_d 0.72 c_bond_d 0.005 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 22.4 c_angle_deg 1.1 c_improper_angle_d 0.72 c_bond_d 0.005 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 157 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing