3MBF

Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MDBPDB entry 3MDB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290BASED ON PACT SCREEN CONDITION F10 WITHOUT NAKHPO4: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 20 MM FRUCTOSE 1,6-BISPHOSPHATE, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
3.3262.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.46α = 90
b = 135.82β = 90
c = 61.54γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.977400SSRLBL7-1

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
12.3728.0399.70.08115.354.42111121046-337.35
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)
12.372.4399.60.4793.24.41557

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3MDB2.3728.032097010220.1670.1650.208To match 3MBD (random)24.84
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]
-1.28-0.441.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg19.307
r_dihedral_angle_3_deg15.33
r_dihedral_angle_1_deg6.078
r_scangle_it3.871
r_scbond_it2.35
r_angle_refined_deg1.499
r_mcangle_it1.36
r_angle_other_deg0.9
r_mcbond_it0.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg19.307
r_dihedral_angle_3_deg15.33
r_dihedral_angle_1_deg6.078
r_scangle_it3.871
r_scbond_it2.35
r_angle_refined_deg1.499
r_mcangle_it1.36
r_angle_other_deg0.9
r_mcbond_it0.711
r_mcbond_other0.169
r_chiral_restr0.083
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2617
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms19

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing