4QPB

Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the absence of phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QP5pdb entry 4QP5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2776 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant (ethylene glycol, PEG 8000)., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0439.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.289α = 90
b = 107.318β = 97.63
c = 34.307γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.783599.10.1677.522.742338923389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8998.80.5862.12.733748

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 4QP51.7833.99233872338770799.190.211330.210250.24432THIN RESOLUTION SHELLS12.819
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]
-1.360.021.61-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.937
r_dihedral_angle_4_deg22.563
r_dihedral_angle_3_deg13.202
r_dihedral_angle_1_deg6.904
r_scangle_it3.932
r_scbond_it2.679
r_angle_refined_deg1.754
r_mcangle_it1.684
r_angle_other_deg1.388
r_mcbond_it1.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.937
r_dihedral_angle_4_deg22.563
r_dihedral_angle_3_deg13.202
r_dihedral_angle_1_deg6.904
r_scangle_it3.932
r_scbond_it2.679
r_angle_refined_deg1.754
r_mcangle_it1.684
r_angle_other_deg1.388
r_mcbond_it1.043
r_chiral_restr0.11
r_bond_refined_d0.023
r_gen_planes_other0.013
r_gen_planes_refined0.01
r_bond_other_d
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2082
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms6

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling