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The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W85 PDB ENTRY 1W85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.5 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.18 α = 90 b = 133.69 β = 90 c = 245.61 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2004-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 20 100 0.08 32.4 9.4 176574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 100 0.82 7.1 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W85 2.3 19.98 128160 6705 100 0.202 0.199 0.1994 0.262 0.2593 RANDOM 41.15
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_1_deg 7.074 r_scangle_it 4.246 r_mcangle_it 3.332 r_scbond_it 2.929 r_mcbond_it 2.281 r_angle_refined_deg 1.209 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_1_deg 7.074 r_scangle_it 4.246 r_mcangle_it 3.332 r_scbond_it 2.929 r_mcbond_it 2.281 r_angle_refined_deg 1.209 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 20626 Nucleic Acid Atoms Solvent Atoms 1173 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing