X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther8CRICrystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M TRIS, 0.2 M CaCl2, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.32α = 90
b = 74.27β = 98.06
c = 92.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.63096.40.089.1323850
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)
12.62.798.80.6732.43.1

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 REPLACEMENTTHROUGHOUT8CRI2.63022646119296.320.236870.234970.27321RANDOM57.491
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]
5.5-9.11-2.72-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.186
r_dihedral_angle_3_deg18.57
r_dihedral_angle_4_deg15.323
r_dihedral_angle_1_deg5.862
r_mcangle_it2.23
r_mcangle_other2.23
r_scangle_other2.069
r_mcbond_it1.563
r_mcbond_other1.561
r_scbond_it1.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.186
r_dihedral_angle_3_deg18.57
r_dihedral_angle_4_deg15.323
r_dihedral_angle_1_deg5.862
r_mcangle_it2.23
r_mcangle_other2.23
r_scangle_other2.069
r_mcbond_it1.563
r_mcbond_other1.561
r_scbond_it1.426
r_scbond_other1.426
r_angle_refined_deg1.291
r_angle_other_deg1.232
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4604
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing