X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1REQPDB ENTRY 1REQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.514.4% PEG 4000, 20% V/V GLYCEROL, 12MM DESULPHO-COA, ADENOSYLCOBALAMIN 16MM,TRIS/HCL 100 MM, PH 7.5 THE 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.
Crystal Properties
Matthews coefficientSolvent content
2.8348

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.398α = 90
b = 161.829β = 90
c = 166.949γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEELLIOTT GX-13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.622997.10.1040.10411.43.4335799654
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.622.7697.10.4460.4463.22.9

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 1REQ2.6229.299776416797.50.2190.2070.283RANDOM48
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]
4.90.20.2
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it6.8
p_mcangle_it4.7
p_mcbond_it2.9
p_scbond_it2.6
p_chiral_restr0.2
p_multtor_nbd0.19
p_singtor_nbd0.13
p_planar_d0.064
p_angle_d0.057
p_bond_d0.016
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it6.8
p_mcangle_it4.7
p_mcbond_it2.9
p_scbond_it2.6
p_chiral_restr0.2
p_multtor_nbd0.19
p_singtor_nbd0.13
p_planar_d0.064
p_angle_d0.057
p_bond_d0.016
p_plane_restr0.016
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_xyhbond_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 Atoms20506
Nucleic Acid Atoms
Solvent Atoms1525
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing