8CRJ

Crystal structure of LplA1 in complex with lipoyl-AMP (Listeria monocytogenes)


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 DROP62930.1 M MES, 1.0 M LiCl, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
4.6173.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.31α = 90
b = 79.31β = 90
c = 225.14γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-08-24MSINGLE 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
12.63098.40.05315.44.522722
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)
12.62.70.6912.44.8

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 REPLACEMENTTHROUGHOUT8CRI2.63021558113598.60.17470.1730.2061RANDOM74.053
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]
-0.79-0.791.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.226
r_dihedral_angle_4_deg14.685
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.166
r_angle_other_deg1.042
r_rigid_bond_restr0.529
r_chiral_restr0.04
r_gen_planes_refined0.003
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.226
r_dihedral_angle_4_deg14.685
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.166
r_angle_other_deg1.042
r_rigid_bond_restr0.529
r_chiral_restr0.04
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2710
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing