3MYO

Crystal structure of tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MYPPDB ENTRY 3MYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62870.1M sodium citrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
3.9869.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.149α = 90
b = 126.149β = 90
c = 148.701γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C11.2399PAL/PLS6C1

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
12.5200.09623.78.14212832.6
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)
2.52.591000.3366.18.14155

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 3MYP2.519.9839947213099.960.201360.200050.2257RANDOM22.794
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]
0.420.42-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_4_deg21.282
r_dihedral_angle_3_deg16.559
r_dihedral_angle_1_deg5.695
r_scangle_it2.701
r_scbond_it1.506
r_angle_refined_deg1.152
r_mcangle_it1.01
r_mcbond_it0.511
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_4_deg21.282
r_dihedral_angle_3_deg16.559
r_dihedral_angle_1_deg5.695
r_scangle_it2.701
r_scbond_it1.506
r_angle_refined_deg1.152
r_mcangle_it1.01
r_mcbond_it0.511
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5132
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling