3R07

Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.629140% v/v MPD, 0.1M sodium acetate, 0.02M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.4264.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.57α = 90
b = 118.57β = 90
c = 72.92γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315rVORTEX FLUORESCENCE DETECTOR2009-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.738.81

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 REPLACEMENTTHROUGHOUT2ARS2.738.81150637891000.20.1980.254RANDOM51.56
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.478
r_dihedral_angle_3_deg19.139
r_dihedral_angle_4_deg17.592
r_dihedral_angle_1_deg6.489
r_scangle_it3.872
r_scbond_it2.427
r_mcangle_it1.742
r_angle_refined_deg1.547
r_mcbond_it1.012
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.478
r_dihedral_angle_3_deg19.139
r_dihedral_angle_4_deg17.592
r_dihedral_angle_1_deg6.489
r_scangle_it3.872
r_scbond_it2.427
r_mcangle_it1.742
r_angle_refined_deg1.547
r_mcbond_it1.012
r_nbtor_refined0.31
r_symmetry_vdw_refined0.244
r_nbd_refined0.22
r_symmetry_hbond_refined0.196
r_xyhbond_nbd_refined0.152
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2761
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms24

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling