7F5I | pdb_00007f5i

X-ray structure of Clostridium perfringens-specific amidase endolysin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LBA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293200 mM potassium bromide, 200 mM potassium thiocyanate, 0.1 M sodium acetate, 3 % w/v poly-gamma-glutamic acid, 5% w/v PEG 3350, pH 5.0)
Crystal Properties
Matthews coefficientSolvent content
2.0840.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.01α = 90
b = 52.87β = 90
c = 58.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2018-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.6518.3699.70.04521.16.3719657
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)
11.651.690.8592

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LBA1.6518.361865895799.760.140090.136670.150.20470.21RANDOM30.658
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]
-0.540.56-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.017
r_dihedral_angle_4_deg22.692
r_dihedral_angle_3_deg17.432
r_scangle_other9.452
r_scbond_it9.062
r_scbond_other8.872
r_long_range_B_refined8.662
r_long_range_B_other8.657
r_dihedral_angle_1_deg7.214
r_mcangle_other5.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.017
r_dihedral_angle_4_deg22.692
r_dihedral_angle_3_deg17.432
r_scangle_other9.452
r_scbond_it9.062
r_scbond_other8.872
r_long_range_B_refined8.662
r_long_range_B_other8.657
r_dihedral_angle_1_deg7.214
r_mcangle_other5.865
r_mcangle_it5.862
r_rigid_bond_restr5.743
r_mcbond_it5.016
r_mcbond_other5.011
r_angle_refined_deg1.514
r_angle_other_deg1.392
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1241
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing