5LP7

Crystal structure of 3-Ketoacyl-CoA Thiolase (MmgA) from Bacillus subtilis.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M sodium iodide, 0.1 M BTP pH 8.5, 20 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.18α = 90
b = 141.12β = 89.98
c = 211.462γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.975DiamondI04

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
12.233.91990.09710.43.1497070161184
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)
12.22.240.41

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 DIFFRACTIONTHROUGHOUT2.231.92153197841298.280.152820.150110.20461RANDOM21.3
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]
2.531.321.48-4.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.704
r_dihedral_angle_4_deg19.093
r_dihedral_angle_3_deg17.586
r_dihedral_angle_1_deg8.264
r_long_range_B_refined5.015
r_long_range_B_other5.015
r_scangle_other2.986
r_mcangle_it2.66
r_mcangle_other2.66
r_angle_refined_deg2.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.704
r_dihedral_angle_4_deg19.093
r_dihedral_angle_3_deg17.586
r_dihedral_angle_1_deg8.264
r_long_range_B_refined5.015
r_long_range_B_other5.015
r_scangle_other2.986
r_mcangle_it2.66
r_mcangle_other2.66
r_angle_refined_deg2.293
r_scbond_it2.014
r_scbond_other2.014
r_mcbond_it1.77
r_mcbond_other1.769
r_angle_other_deg1.224
r_chiral_restr0.169
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms21815
Nucleic Acid Atoms
Solvent Atoms878
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing