X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME B12) AND 12MM DESULPHO-COA (FINAL CONCENTRATIONS), EQUILIBRATED AGAINST 14% W/V PEG 4000 AND 20% V/V GLYCEROL, 100MM TRIS PH 7.5. THE ELECTRON DENSITY MAPS SHOW NO ADENOSYL GROUP ATTACHED TO THE COBALT ATOM, AND SPECTRA FROM SIMILAR CRYSTALS SHOW EVIDENCE OF SUBSTANTIAL REDUCTION OF COIII TO COII, WHICH IS 5-COORDINATE. THE COBALAMIN IN THIS CRYSTAL STRUCTURE IS BEST CONSIDERED AS REDUCED COB(II)ALAMIN (OR B12R). THE BOND LENGTH FROM THE COBALT TO THE LOWER AXIAL LIGAND, NE2 OF HIS A 610 (OR HIS C 610) IS SIGNIFICANTLY LONGER THAN THAT IN MODEL COMPOUNDS. POORLY ORDERED LOOPS: DENSITY IN THE FOLLOWING REGIONS IS POOR, AND THE MODEL MUST BE CONSIDERED UNRELIABLE. ALPHA CHAIN: A 1, C 1 MISSING, A 2 - A 3, C 2 - C 3 WEAK. BETA CHAIN: B 1 - C 19, C 1 - C 16 MISSING; B 184 - B 191, D 184 - D 191 WEAK; D 228 - D 230 WEAK; D 271 - D 276 VERY POOR DENSITY (MUCH BETTER IN CHAIN B); D 315 WEAK; D 474 - D 428 WEAK.
Crystal Properties
Matthews coefficientSolvent content
2.7648

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.8α = 90
b = 161.3β = 105.1
c = 88.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMAR scanner 300 mm plate1994-06-24M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID2ESRFID2

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
122099.80.0514.62173775

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTION2202063271090799.80.220.27542
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
p_scangle_it5.8
p_scbond_it4.6
p_mcangle_it4.1
p_mcbond_it3.2
p_multtor_nbd0.256
p_xyhbond_nbd0.187
p_singtor_nbd0.183
p_chiral_restr0.156
p_planar_d0.044
p_angle_d0.039
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it5.8
p_scbond_it4.6
p_mcangle_it4.1
p_mcbond_it3.2
p_multtor_nbd0.256
p_xyhbond_nbd0.187
p_singtor_nbd0.183
p_chiral_restr0.156
p_planar_d0.044
p_angle_d0.039
p_bond_d0.017
p_plane_restr0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20510
Nucleic Acid Atoms
Solvent Atoms1532
Heterogen Atoms330

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction