4EF1

Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627720.0% iso-Propanol, 20.0% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.923α = 90
b = 96.485β = 100.55
c = 69.042γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2012-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
11.929.3892.40.06210.0439597-318.401
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)
11.91.9791.80.3532.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.929.3839575199097.760.19090.18840.2382RANDOM29.8156
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]
2.380.73-2.130.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.344
r_dihedral_angle_3_deg11.262
r_dihedral_angle_4_deg8.299
r_dihedral_angle_1_deg4.903
r_angle_refined_deg1.619
r_angle_other_deg1.32
r_symmetry_vdw_refined0.253
r_nbd_refined0.242
r_nbd_other0.208
r_symmetry_vdw_other0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.344
r_dihedral_angle_3_deg11.262
r_dihedral_angle_4_deg8.299
r_dihedral_angle_1_deg4.903
r_angle_refined_deg1.619
r_angle_other_deg1.32
r_symmetry_vdw_refined0.253
r_nbd_refined0.242
r_nbd_other0.208
r_symmetry_vdw_other0.196
r_nbtor_refined0.167
r_nbtor_other0.11
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3840
Nucleic Acid Atoms
Solvent Atoms529
Heterogen Atoms18

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction