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Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JEH 1JEH (CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.411 α = 90 b = 105.76 β = 92.65 c = 84.907 γ = 90
Symmetry Space Group P 1 21 1
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 2004-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.67 50 98.6 0.037 12.7 104936
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 1.7 1.76 99 0.194 2.3
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 1JEH (CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE) 1.7 32.62 94396 10510 99.7 0.19853 0.19504 0.2068 0.22988 0.2386 RANDOM 17.657
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 Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.499 r_scangle_it 2.572 r_scbond_it 1.464 r_angle_refined_deg 1.104 r_angle_other_deg 0.84 r_mcangle_it 0.825 r_mcbond_it 0.432 r_nbd_other 0.232 r_symmetry_vdw_other 0.219 r_nbd_refined 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.499 r_scangle_it 2.572 r_scbond_it 1.464 r_angle_refined_deg 1.104 r_angle_other_deg 0.84 r_mcangle_it 0.825 r_mcbond_it 0.432 r_nbd_other 0.232 r_symmetry_vdw_other 0.219 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.094 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.078 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6914 Nucleic Acid Atoms Solvent Atoms 972 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing