5UOS

Crystal Structure of CblC (MMACHC) (1-238), a human B12 processing enzyme, complexed with an Antivitamin B12


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SC0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52770.2 M NaCl, 0.1 M CHES:NaOH pH 9.5, 1.26 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
5.2576.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.432α = 90
b = 114.432β = 90
c = 150.631γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2016-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03318APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rpim I (All)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
12.5199.186.30.0940.0980.0270.99821.212.317391
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.512.6287.80.6910.7210.1980.8533.811.7

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 REPLACEMENTTHROUGHOUT3SC02.5199.11652786384.920.178320.176450.21384RANDOM51.619
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]
-1.37-0.69-1.374.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.989
r_dihedral_angle_3_deg14.954
r_dihedral_angle_4_deg11.333
r_dihedral_angle_1_deg7.748
r_long_range_B_refined7.679
r_mcangle_it4.259
r_scbond_it3.713
r_mcbond_it2.704
r_angle_refined_deg1.178
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.989
r_dihedral_angle_3_deg14.954
r_dihedral_angle_4_deg11.333
r_dihedral_angle_1_deg7.748
r_long_range_B_refined7.679
r_mcangle_it4.259
r_scbond_it3.713
r_mcbond_it2.704
r_angle_refined_deg1.178
r_chiral_restr0.072
r_bond_refined_d0.013
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_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 Atoms1928
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing