4MJX

Crystal structure of the double mutant (S112A, H303A) of B.anthracis mycrocine immunity protein (MccF)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GJZPDB ENTRY 3GJZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92891.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.652.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.382α = 90
b = 118.382β = 90
c = 56.249γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rdouble crystal2013-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
11.44099.70.074203.515731415273222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4299.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GJZ1.428.7322152699145030766999.680.120.112080.110170.14826RANDOM20.065
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]
-0.41-0.410.82
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.094
r_dihedral_angle_2_deg35.453
r_dihedral_angle_4_deg21.506
r_sphericity_bonded17.077
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg6.272
r_rigid_bond_restr5.703
r_angle_refined_deg1.956
r_angle_other_deg0.985
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.094
r_dihedral_angle_2_deg35.453
r_dihedral_angle_4_deg21.506
r_sphericity_bonded17.077
r_dihedral_angle_3_deg11.281
r_dihedral_angle_1_deg6.272
r_rigid_bond_restr5.703
r_angle_refined_deg1.956
r_angle_other_deg0.985
r_chiral_restr0.135
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5317
Nucleic Acid Atoms
Solvent Atoms928
Heterogen Atoms16

Software

Software
Software NamePurpose
SBC-Collectdata collection
MolProbitymodel building
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing