2IXU

Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (wild-type endolysin)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H09PDB ENTRY 1H09

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.1761.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.521α = 90
b = 96.504β = 90
c = 127.317γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2003-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS

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
12.2825.8699.90.076.69.3326781.5
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)
12.262.4199.50.431.89.1

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 1H092.2825.3221331157399.710.212360.212360.26238RANDOM36.773
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]
1.69-1.56-0.13
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.956
c_scbond_it2.667
c_mcangle_it2.101
c_angle_deg1.566
c_mcbond_it1.145
c_bond_d0.021
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it3.956
c_scbond_it2.667
c_mcangle_it2.101
c_angle_deg1.566
c_mcbond_it1.145
c_bond_d0.021
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
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2763
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms51

Software

Software
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing