5KYM

Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318-22% (w/v) polyethylene glycol 3350 (PEG3350), 0.1 M HEPES, and 0.2 M MgCl 2
Crystal Properties
Matthews coefficientSolvent content
3.8167.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.836α = 90
b = 173.836β = 90
c = 173.836γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2012-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.846.4699.940.18790.99610.18921613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.8022.90199.580.1670.64.6

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 DIFFRACTIONSADTHROUGHOUT2.846.4619924167499.930.223590.219110.27703RANDOM79.442
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg23.655
r_dihedral_angle_3_deg16.868
r_long_range_B_refined9.762
r_long_range_B_other9.761
r_scangle_other7.963
r_dihedral_angle_1_deg6.558
r_mcangle_it6.301
r_mcangle_other6.301
r_scbond_it4.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.712
r_dihedral_angle_4_deg23.655
r_dihedral_angle_3_deg16.868
r_long_range_B_refined9.762
r_long_range_B_other9.761
r_scangle_other7.963
r_dihedral_angle_1_deg6.558
r_mcangle_it6.301
r_mcangle_other6.301
r_scbond_it4.801
r_scbond_other4.8
r_mcbond_it3.977
r_mcbond_other3.964
r_angle_refined_deg2.009
r_angle_other_deg1.064
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3859
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms278

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing