2DJ5

Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TJNPDB ENTRY 1TJN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82981.9M ammonium phosphate pH6.8, 4% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.8156.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.721α = 90
b = 62.721β = 90
c = 150.609γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.019943ALS8.3.1

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
12.560690.0612.81251786371.91.9
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)
12.52.5948.90.2651.9

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1TJN2.5554.311184792540970.90.2150.2150.2120.267RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.832
r_dihedral_angle_3_deg19.095
r_scangle_it17.282
r_dihedral_angle_4_deg13.657
r_scbond_it12.934
r_mcangle_it9.358
r_mcbond_it6.79
r_dihedral_angle_1_deg6.602
r_angle_refined_deg1.479
r_symmetry_hbond_refined0.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.832
r_dihedral_angle_3_deg19.095
r_scangle_it17.282
r_dihedral_angle_4_deg13.657
r_scbond_it12.934
r_mcangle_it9.358
r_mcbond_it6.79
r_dihedral_angle_1_deg6.602
r_angle_refined_deg1.479
r_symmetry_hbond_refined0.414
r_symmetry_vdw_refined0.364
r_nbtor_refined0.318
r_nbd_refined0.236
r_xyhbond_nbd_refined0.186
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2020
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms38

Software

Software
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling