1W85

The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QS0PDB ENTRY 1QS0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529310% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00
Crystal Properties
Matthews coefficientSolvent content
2.2144.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.27α = 90
b = 232.33β = 90.81
c = 91.924γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-05-20MSINGLE 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
122094.60.0713.83171898
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)
122.0768.40.262.7

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 1QS0220171898903194.80.1780.1760.215RANDOM21.98
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]
1.86-0.32-0.46-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.773
r_dihedral_angle_4_deg18.551
r_dihedral_angle_3_deg15.833
r_dihedral_angle_1_deg5.532
r_angle_refined_deg1.352
r_mcangle_it0.645
r_scangle_it0.587
r_mcbond_it0.408
r_scbond_it0.393
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.773
r_dihedral_angle_4_deg18.551
r_dihedral_angle_3_deg15.833
r_dihedral_angle_1_deg5.532
r_angle_refined_deg1.352
r_mcangle_it0.645
r_scangle_it0.587
r_mcbond_it0.408
r_scbond_it0.393
r_nbtor_refined0.308
r_symmetry_vdw_refined0.209
r_nbd_refined0.206
r_chiral_restr0.138
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.125
r_metal_ion_refined0.074
r_bond_refined_d0.014
r_gen_planes_refined0.001
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_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 Atoms21642
Nucleic Acid Atoms
Solvent Atoms1733
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing