9HGK | pdb_00009hgk

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229210% v/v EtOH, 0.1 M sodium-citrate pH 4.2, 1% w/w PEG 1000
Crystal Properties
Matthews coefficientSolvent content
2.1743.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.96α = 90
b = 74.96β = 90
c = 183.99γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2024-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5564.941000.999817.6420.287936
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)
11.551.580.3264

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.653.0473899385697.280.237890.234840.23490.298950.2987RANDOM57.637
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]
1.180.591.18-3.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.657
r_long_range_B_refined15.823
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg14.541
r_mcangle_it11.949
r_scbond_it11.034
r_mcbond_it9.628
r_dihedral_angle_1_deg6.205
r_angle_refined_deg1.246
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.657
r_long_range_B_refined15.823
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg14.541
r_mcangle_it11.949
r_scbond_it11.034
r_mcbond_it9.628
r_dihedral_angle_1_deg6.205
r_angle_refined_deg1.246
r_chiral_restr0.094
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms4503
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing