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Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D2K PDB ENTRY 1D2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.5 1.4 M LI2SO4 0.1 M TRIS PH 9.5
Crystal Properties Matthews coefficient Solvent content 3.63 66.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.704 α = 90 b = 117.704 β = 90 c = 99.783 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD MARRESEACH MIRRORS 2003-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 20 96.6 0.08 8.3 3.1 88304 2 17.4
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 2 2.07 79.2 0.4 2.3 2.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1D2K 2 19.82 88301 4436 96.3 0.224 0.224 0.2111 0.248 0.2354 RANDOM 25.3
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] 0.7 0.7 -1.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 2.97 c_scbond_it 2.23 c_mcangle_it 1.98 c_mcbond_it 1.44 c_angle_deg 1.3 c_improper_angle_d 0.74 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 2.97 c_scbond_it 2.23 c_mcangle_it 1.98 c_mcbond_it 1.44 c_angle_deg 1.3 c_improper_angle_d 0.74 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6237 Nucleic Acid Atoms Solvent Atoms 1080 Heterogen Atoms 30
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing