4UOP

Crystal structure of the lipoteichoic acid synthase LtaP from Listeria monocytogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W5QPDB ENTRY 2W5Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4100MM NA CACODYLATE PH 5.4, 100MM MGCL2, 33% PEG2000
Crystal Properties
Matthews coefficientSolvent content
2.0840.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.198α = 71.63
b = 53.7β = 76.78
c = 85.037γ = 65.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 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
11.7547.9694.80.0710.73.8770132
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)
11.751.8492.60.52.53.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2W5Q1.7580.273165384794.790.179710.178260.20738RANDOM30.899
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]
-2.58-0.421.152.1-0.69-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.205
r_dihedral_angle_4_deg18.609
r_dihedral_angle_3_deg12.325
r_dihedral_angle_1_deg5.921
r_mcangle_it2.534
r_scbond_it2.071
r_mcbond_it1.587
r_mcbond_other1.585
r_angle_refined_deg1.187
r_angle_other_deg0.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.205
r_dihedral_angle_4_deg18.609
r_dihedral_angle_3_deg12.325
r_dihedral_angle_1_deg5.921
r_mcangle_it2.534
r_scbond_it2.071
r_mcbond_it1.587
r_mcbond_other1.585
r_angle_refined_deg1.187
r_angle_other_deg0.857
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6596
Nucleic Acid Atoms
Solvent Atoms481
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing