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Crystal Structure of the Dihydrolipoamide Dehydrogenase (E3)-Binding Domain of Human E3-Binding Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F5Z PDB ENTRY 2F5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 293 1.35 M sodium citrate, 0.075% beta-octyl-glucopyranoside, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30
Crystal Properties Matthews coefficient Solvent content 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.845 α = 90 b = 36.845 β = 90 c = 191.542 γ = 120
Symmetry Space Group P 65 2 2
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 QUANTUM 315 2004-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 28.5 98.9 0.032 67.8 13.7 12109 -3 23.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 95.4 0.148 8.6 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2F5Z 1.55 28.5 12109 12034 584 98.9 0.206 0.206 0.2208 0.223 0.2414 RANDOM 26
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] 1.58 2.75 1.58 -3.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_angle_deg 2.7 c_improper_angle_d 1.8 c_bond_d 0.033 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_angle_deg 2.7 c_improper_angle_d 1.8 c_bond_d 0.033 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 470 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHASER phasing CNS refinement HKL-2000 data reduction