5UJC

Crystal structure of a C.elegans B12-trafficking protein CblC, a human MMACHC homologue


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527721.5% PEG 3350, 40 mM Spermidine-HCl, 0.2 M (NH4)2tartarate
Crystal Properties
Matthews coefficientSolvent content
2.6152.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.008α = 90
b = 66.089β = 90
c = 92.826γ = 90
Symmetry
Space GroupP 21 21 21

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 focusing2014-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03325APS23-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
11.3553.8492.90.0540.0620.0290.997153.86679912
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)
11.351.3758.70.5730.7220.4350.6181.92.3

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 REPLACEMENTTHROUGHOUT3SBZ1.3553.8463476328592.280.133610.132090.16303RANDOM18.25
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]
-0.921.79-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.461
r_sphericity_bonded13.967
r_dihedral_angle_4_deg12.944
r_dihedral_angle_3_deg11.867
r_dihedral_angle_1_deg5.93
r_long_range_B_refined3.992
r_long_range_B_other3.615
r_scangle_other3.447
r_scbond_it2.902
r_scbond_other2.902
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.461
r_sphericity_bonded13.967
r_dihedral_angle_4_deg12.944
r_dihedral_angle_3_deg11.867
r_dihedral_angle_1_deg5.93
r_long_range_B_refined3.992
r_long_range_B_other3.615
r_scangle_other3.447
r_scbond_it2.902
r_scbond_other2.902
r_mcangle_it2.713
r_mcangle_other2.713
r_rigid_bond_restr2.233
r_mcbond_other2.195
r_mcbond_it2.194
r_angle_refined_deg2.013
r_angle_other_deg0.736
r_chiral_restr0.541
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.003
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2184
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing