6JIS

Crystal structure of the histidine racemase CntK in cobalt and nickel transporter system of staphylococcus aureus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% pEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.4745.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.85α = 90
b = 60.374β = 116.09
c = 76.755γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS EIGER R 4M2018-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9792SSRFBL17U1

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
11.8232.2496.80.112.94.425303
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)
11.821.860.4834.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6JIW1.8232.2424057124596.510.197970.195450.24861RANDOM21.533
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]
2.570.84-1.65-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.714
r_dihedral_angle_4_deg21.704
r_dihedral_angle_3_deg12.975
r_dihedral_angle_1_deg6.898
r_long_range_B_refined5.736
r_long_range_B_other5.593
r_scangle_other3.55
r_mcangle_it2.697
r_mcangle_other2.696
r_scbond_it2.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.714
r_dihedral_angle_4_deg21.704
r_dihedral_angle_3_deg12.975
r_dihedral_angle_1_deg6.898
r_long_range_B_refined5.736
r_long_range_B_other5.593
r_scangle_other3.55
r_mcangle_it2.697
r_mcangle_other2.696
r_scbond_it2.271
r_scbond_other2.27
r_mcbond_it1.726
r_mcbond_other1.726
r_angle_refined_deg1.405
r_angle_other_deg1.353
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2029
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing