3MBD

Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QO5PDB ENTRY 1QO5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529090% PACT SCREEN CONDITION F10, 10% ADDITIVE SCREEN G12: 90MM BIS-TRIS PROPANE PH 6.5, 18% PEG 3350, 18 MM NAKHPO4, 10 MM UREA, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
3.4163.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.96α = 90
b = 137.61β = 90
c = 62.23γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
1236.899.80.05621.836.23579235720-3
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)
122.0599.30.4893.66.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1QO5235.343579233882174999.580.163750.16240.19021RANDOM29.39
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]
-0.54-0.981.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.385
r_dihedral_angle_4_deg22.125
r_dihedral_angle_3_deg13.748
r_dihedral_angle_1_deg5.804
r_scangle_it3.645
r_scbond_it2.234
r_angle_refined_deg1.395
r_mcangle_it1.371
r_angle_other_deg0.913
r_mcbond_it0.763
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.385
r_dihedral_angle_4_deg22.125
r_dihedral_angle_3_deg13.748
r_dihedral_angle_1_deg5.804
r_scangle_it3.645
r_scbond_it2.234
r_angle_refined_deg1.395
r_mcangle_it1.371
r_angle_other_deg0.913
r_mcbond_it0.763
r_mcbond_other0.208
r_chiral_restr0.09
r_bond_refined_d0.015
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 Atoms2631
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms6

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling