2XVX

Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris Hildenborough (Native)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherMODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 2UL OF CRYSTALLIZATION SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
3.666.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.062α = 90
b = 121.062β = 90
c = 120.246γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2007-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.942.899.90.087.6283536525.5
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)
11.9299.20.830.920.3

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 REPLACEMENTTHROUGHOUTMODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT.1.985.633596176899.860.174770.173510.19875RANDOM29.552
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]
-0.3-0.30.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.235
r_dihedral_angle_4_deg19.06
r_dihedral_angle_3_deg13.18
r_dihedral_angle_1_deg5.154
r_scangle_it4.967
r_scbond_it3.044
r_mcangle_it2.075
r_angle_refined_deg1.767
r_mcbond_it1.145
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.235
r_dihedral_angle_4_deg19.06
r_dihedral_angle_3_deg13.18
r_dihedral_angle_1_deg5.154
r_scangle_it4.967
r_scbond_it3.044
r_mcangle_it2.075
r_angle_refined_deg1.767
r_mcbond_it1.145
r_chiral_restr0.122
r_bond_refined_d0.02
r_gen_planes_refined0.009
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_other
r_long_range_B_refined
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 Atoms1979
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing