9HGO | pdb_00009hgo

Crystal Structure of the Coxiella burnetii E110Q Mutant 2-methylisocitrate lyase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9HGK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.229210% v/v EtOH, 0.1 M sodium-citrate pH 4.2, 1% w/w PEG 1000
Crystal Properties
Matthews coefficientSolvent content
2.1342.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.18α = 90
b = 74.18β = 90
c = 184.45γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2024-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9999DiamondI24

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
11.8261.4896.40.995213.328.751772
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)
11.821.860.3443

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 REPLACEMENTTHROUGHOUT1.8261.4848649259395.440.23550.232110.23210.298890.2988RANDOM55.033
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]
0.850.420.85-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_long_range_B_refined16.499
r_dihedral_angle_3_deg15.674
r_dihedral_angle_4_deg13.658
r_scbond_it12.887
r_mcangle_it12.404
r_mcbond_it10.502
r_dihedral_angle_1_deg6.247
r_angle_refined_deg1.475
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_long_range_B_refined16.499
r_dihedral_angle_3_deg15.674
r_dihedral_angle_4_deg13.658
r_scbond_it12.887
r_mcangle_it12.404
r_mcbond_it10.502
r_dihedral_angle_1_deg6.247
r_angle_refined_deg1.475
r_chiral_restr0.118
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms4475
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing