1W88

The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W85PDB ENTRY 1W85

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1515% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
2.549.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.18α = 90
b = 133.69β = 90
c = 245.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.1201000.0832.49.4176574
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)
12.12.171000.827.19.4

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 1W852.319.9812816067051000.2020.1990.262RANDOM41.15
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.643
r_dihedral_angle_4_deg15.736
r_dihedral_angle_3_deg15.49
r_dihedral_angle_1_deg7.074
r_scangle_it4.246
r_mcangle_it3.332
r_scbond_it2.929
r_mcbond_it2.281
r_angle_refined_deg1.209
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.643
r_dihedral_angle_4_deg15.736
r_dihedral_angle_3_deg15.49
r_dihedral_angle_1_deg7.074
r_scangle_it4.246
r_mcangle_it3.332
r_scbond_it2.929
r_mcbond_it2.281
r_angle_refined_deg1.209
r_nbtor_refined0.304
r_symmetry_hbond_refined0.225
r_nbd_refined0.198
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.156
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms20626
Nucleic Acid Atoms
Solvent Atoms1173
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing