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A 2.4 crystal structure of conkunitzin-S1, a novel Kunitz-fold cone snail neurotoxin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DTX ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX experimental model PDB 1KNT ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX experimental model PDB 2PTC ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX experimental model PDB 1TFX ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291 PEG-400, ammonium sulfate, sodium azide, acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.756 α = 119.92 b = 51.543 β = 107.52 c = 51.6 γ = 91.14
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Nonius Kappa CCD Nonius FR591 High brilliance 2004-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.45 20 99 0.098 4 15511 15238 -3 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.45 2.54 97.8 0.365 3.8 3.8 1498
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX 2.45 20 -3 15511 15238 1208 98.3 0.232 0.232 0.221 0.2271 0.255 0.2566 RANDOM, 8% 23.9
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_scangle_it 3.89 c_scbond_it 2.74 c_mcangle_it 2.67 c_mcbond_it 1.75 c_angle_deg 1.44 c_bond_d 0.0085 c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2694 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 75
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing