1W9V

Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus fumigatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D2KPDB ENTRY 1D2K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19.51.4 M LI2SO4 0.1 M TRIS PH 9.5
Crystal Properties
Matthews coefficientSolvent content
3.6366.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.704α = 90
b = 117.704β = 90
c = 99.783γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARRESEACHMIRRORS2003-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
122096.60.088.33.188304217.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0779.20.42.32.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1D2K219.8288301443696.30.2240.2240.248RANDOM25.3
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]
0.70.7-1.4
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.5
c_scangle_it2.97
c_scbond_it2.23
c_mcangle_it1.98
c_mcbond_it1.44
c_angle_deg1.3
c_improper_angle_d0.74
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.5
c_scangle_it2.97
c_scbond_it2.23
c_mcangle_it1.98
c_mcbond_it1.44
c_angle_deg1.3
c_improper_angle_d0.74
c_bond_d0.005
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 AtomsNumber
Protein Atoms6237
Nucleic Acid Atoms
Solvent Atoms1080
Heterogen Atoms30

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing