X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X2GLipoate protein ligase A from E. coli

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293ethylene glycol, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
358.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 111.6β = 90
c = 289.6γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040mirror2004-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.92154SPring-8BL44XU

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
12.920097.40.1215.652924729247-3
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)
2.93990.4213.82939

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDifference FourierTHROUGHOUTLipoate protein ligase A from E. coli2.9166.672766627666153397.10.19070.19070.18630.2714RANDOM39.469
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]
0.59-0.05-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.855
r_dihedral_angle_3_deg21.67
r_dihedral_angle_4_deg19.997
r_dihedral_angle_1_deg8.038
r_scangle_it3.692
r_scbond_it2.238
r_angle_refined_deg1.976
r_mcangle_it1.467
r_mcbond_it0.845
r_nbtor_refined0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.855
r_dihedral_angle_3_deg21.67
r_dihedral_angle_4_deg19.997
r_dihedral_angle_1_deg8.038
r_scangle_it3.692
r_scbond_it2.238
r_angle_refined_deg1.976
r_mcangle_it1.467
r_mcbond_it0.845
r_nbtor_refined0.329
r_nbd_refined0.254
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.169
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.006
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 Atoms7891
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling