4QP5

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LXCPDB ENTRY 4LXC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.05 M potassium dihydrogen phosphate, 20 % w/v PEG 8000 and 6 mM glycine hydroxamate supplemented with 10% (v/v) glycerol for cryocooling. Crystal was soaked for 5 min with 25 mM iodo-GGSGG pentapeptide dissolved in the buffer used for cryocooling, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.279α = 90
b = 106.78β = 97.42
c = 34.331γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.2635.698.30.07213.235.7764943
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)
11.261.3390.90.4122.494.47

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4LXC1.2634.041.426490264902203998.30.1330.130.175
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]
-1.95571.06073.6445-1.6888
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.654
f_angle_d1.153
f_chiral_restr0.074
f_bond_d0.01
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2086
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms24

Software

Software
Software NamePurpose
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling