4EF2

Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.529330.0% polyethylene glycol 400, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.225α = 90
b = 75.691β = 90
c = 143.815γ = 90
Symmetry
Space GroupP 21 21 21

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)2012-02-08MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97966,0.97901SSRLBL11-1

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
12.128.76390.60.0412.3728845-338.876
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)
12.12.1764.90.7461.4

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 DIFFRACTIONMADTHROUGHOUT2.128.76328794145895.250.18980.18750.2322RANDOM52.5789
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]
-3.82-0.874.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_4_deg14.003
r_dihedral_angle_3_deg12.346
r_dihedral_angle_1_deg5.359
r_angle_refined_deg1.858
r_angle_other_deg1.465
r_nbd_other0.215
r_nbd_refined0.214
r_nbtor_refined0.171
r_symmetry_vdw_other0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_4_deg14.003
r_dihedral_angle_3_deg12.346
r_dihedral_angle_1_deg5.359
r_angle_refined_deg1.858
r_angle_other_deg1.465
r_nbd_other0.215
r_nbd_refined0.214
r_nbtor_refined0.171
r_symmetry_vdw_other0.14
r_symmetry_vdw_refined0.122
r_nbtor_other0.108
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3746
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms68

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing