2IYO

Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PGDPDB ENTRY 2PGD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.225% PEG 3350, 300MM AMMONIUM ACCETATE, 0.1M SODIUM CACODYLATE, pH 7.20
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.582α = 90
b = 60.582β = 90
c = 243.128γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2004-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.420960.0613.75.519558
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)
12.42.5750.156.72.2

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 2PGD2.419.83185551003960.1620.1590.221RANDOM27.6
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.893
r_dihedral_angle_4_deg17.345
r_dihedral_angle_3_deg16.757
r_dihedral_angle_1_deg5.213
r_scangle_it1.978
r_scbond_it1.204
r_angle_refined_deg1.155
r_mcangle_it0.829
r_mcbond_it0.48
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.893
r_dihedral_angle_4_deg17.345
r_dihedral_angle_3_deg16.757
r_dihedral_angle_1_deg5.213
r_scangle_it1.978
r_scbond_it1.204
r_angle_refined_deg1.155
r_mcangle_it0.829
r_mcbond_it0.48
r_nbtor_refined0.3
r_nbd_refined0.191
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.139
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms3672
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing