5SY4

Atomic resolution structure of reduced E. coli YajL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298polyethylene glycol 4000, Tris HCl, magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.0339.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.875α = 90
b = 78.313β = 90
c = 99.434γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MRh coated collimating mirrors, K-B focusing mirrors2015-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.73SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
10.983897.60.085115.910.2191363
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.981962.3930.4791.19.5

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 REPLACEMENTTHROUGHOUT2AB00.9861.52187313384297.340.114270.114030.1266RANDOM12.354
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]
0.03-0.10.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.477
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg14.352
r_dihedral_angle_3_deg10.834
r_sphericity_bonded8.706
r_dihedral_angle_1_deg6.254
r_rigid_bond_restr3.449
r_long_range_B_refined3.171
r_long_range_B_other2.487
r_scangle_other2.119
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.477
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg14.352
r_dihedral_angle_3_deg10.834
r_sphericity_bonded8.706
r_dihedral_angle_1_deg6.254
r_rigid_bond_restr3.449
r_long_range_B_refined3.171
r_long_range_B_other2.487
r_scangle_other2.119
r_angle_refined_deg1.937
r_scbond_it1.797
r_scbond_other1.745
r_mcangle_other1.449
r_mcangle_it1.448
r_angle_other_deg1.183
r_mcbond_it1.059
r_mcbond_other1.049
r_chiral_restr0.164
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2902
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing