3T2D

Fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus, FBP-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T2BPDB ENTRY 3T2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52948% PEG3350, 0.1 M HEPES/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.6253.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.291α = 90
b = 112.291β = 90
c = 151.348γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELPSI PILATUS 6M2010-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

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
11.3654.7899.90.0730.07318.59.210310710298122
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)
11.361.3999.90.4240.4245.18.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 3T2B1.3654.7829783497834514799.870.104750.103640.1259RANDOM
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]
0.080.08-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.014
r_dihedral_angle_4_deg17.468
r_dihedral_angle_3_deg14.154
r_scangle_it8.104
r_dihedral_angle_1_deg6.644
r_scbond_it5.677
r_mcangle_it3.695
r_mcbond_it2.56
r_rigid_bond_restr2.512
r_angle_refined_deg2.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.014
r_dihedral_angle_4_deg17.468
r_dihedral_angle_3_deg14.154
r_scangle_it8.104
r_dihedral_angle_1_deg6.644
r_scbond_it5.677
r_mcangle_it3.695
r_mcbond_it2.56
r_rigid_bond_restr2.512
r_angle_refined_deg2.365
r_angle_other_deg1.178
r_mcbond_other0.908
r_chiral_restr0.159
r_bond_refined_d0.031
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3057
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms24

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling