2XVY

Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XVZPDB ENTRY 2XVZ

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 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0.2UL OF COBALT CHLORIDE IN AEROBIC CONDITIONS.
Crystal Properties
Matthews coefficientSolvent content
3.665.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.81α = 90
b = 120.81β = 90
c = 119.71γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHCOLLIMATING RHODIUM COATED MIRROR (BEFORE MONOCHROMATOR) AND FOCUSSING TOROIDAL RHODIUM COATED MIRROR (AFTER MONOCHROMATOR)2007-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.749.2496.70.0420.85.44683030.5
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)
11.71.8184.40.462.94.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XVZ1.785.4444493237996.790.172960.172150.18779RANDOM25.875
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]
-0.43-0.430.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.72
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg5.026
r_scangle_it4.83
r_scbond_it3.036
r_mcangle_it1.915
r_angle_refined_deg1.762
r_mcbond_it1.088
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.72
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg5.026
r_scangle_it4.83
r_scbond_it3.036
r_mcangle_it1.915
r_angle_refined_deg1.762
r_mcbond_it1.088
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms238
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing