3TLY

Microcin C7 self immunity protein MccF active site mutant S118A/N220A/K247A in the apo state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TLAPDB ENTRY 3TLA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528210% PEG 8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
2.0138.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.422α = 90
b = 85.658β = 101.24
c = 73.016γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-DAPS21-ID-D

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
11.69501000.06313.76.173757
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)
11.691.7299.90.215.53676

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 3TLA1.72572175365299.980.17310.17160.2008RANDOM15.1957
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]
-0.470.070.97-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg11.185
r_dihedral_angle_1_deg5.346
r_scangle_it1.951
r_scbond_it1.108
r_angle_other_deg1.036
r_angle_refined_deg0.988
r_mcangle_it0.625
r_mcbond_it0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg11.185
r_dihedral_angle_1_deg5.346
r_scangle_it1.951
r_scbond_it1.108
r_angle_other_deg1.036
r_angle_refined_deg0.988
r_mcangle_it0.625
r_mcbond_it0.306
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5246
Nucleic Acid Atoms
Solvent Atoms920
Heterogen Atoms24

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction