9HHY | pdb_00009hhy

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Inhibitor Isocitric Acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH292Clear Strategy I D7: 0.3 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5, 8% w/v PEG 20,000, 8% v/v PEG 500 MME
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.785α = 90
b = 115.55β = 92.34
c = 195.241γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-12-13MSINGLE 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
12.3359.2499.980.99458.297.04177721
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)
12.332.370.2991

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 REPLACEMENTTHROUGHOUT2.3359.24168617884199.830.216570.2140.2140.265230.2653RANDOM68.925
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]
2.571.57-1.87-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_long_range_B_refined21.983
r_mcangle_it18.71
r_dihedral_angle_4_deg17.295
r_scbond_it15.816
r_dihedral_angle_3_deg14.783
r_mcbond_it14.276
r_dihedral_angle_1_deg6.113
r_angle_refined_deg1.195
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_long_range_B_refined21.983
r_mcangle_it18.71
r_dihedral_angle_4_deg17.295
r_scbond_it15.816
r_dihedral_angle_3_deg14.783
r_mcbond_it14.276
r_dihedral_angle_1_deg6.113
r_angle_refined_deg1.195
r_chiral_restr0.096
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 Atoms26526
Nucleic Acid Atoms
Solvent Atoms881
Heterogen Atoms326

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing