2YCE

Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OJXPDB ENTRY 1OJX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
159% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL, 100 MM FBP
Crystal Properties
Matthews coefficientSolvent content
240

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.9α = 90
b = 159.2β = 107.8
c = 101.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.934097.30.0816.24.2179009-3
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)
11.932.0277.60.372.22.5

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 1OJX1.9339.817900927231000.156540.155920.19811RANDOM22.83
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]
-0.02-0.060.06-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.855
r_dihedral_angle_3_deg14.504
r_dihedral_angle_1_deg5.722
r_scangle_it3.395
r_scbond_it2.158
r_angle_refined_deg1.485
r_mcangle_it1.125
r_mcbond_it0.657
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.855
r_dihedral_angle_3_deg14.504
r_dihedral_angle_1_deg5.722
r_scangle_it3.395
r_scbond_it2.158
r_angle_refined_deg1.485
r_mcangle_it1.125
r_mcbond_it0.657
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.007
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_other
r_long_range_B_refined
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 Atoms19381
Nucleic Acid Atoms
Solvent Atoms1518
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing