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The structure of dihydrolipoamide dehydrogenase from Colwellia psychrerythraea 34H.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 0.1M Bis-tris,
20%(w/v) PEG MME5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.06 59.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.497 α = 90 b = 246.353 β = 90.2 c = 73.664 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 ADSC QUANTUM 315 mirror 2009-04-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937, 0.97953 APS 19-ID
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 2.15 44 99.1 0.107 17.6 3.6 138959 138959 36.45
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 2.15 2.19 93.6 0.46 2.2 3 6506
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.15 43.9 131911 131911 6975 98.86 0.1885 0.1885 0.18612 0.1876 0.23338 0.2338 RANDOM 27.825
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] -0.1 0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.346 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 17.335 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.052 r_scbond_it 2.023 r_angle_refined_deg 1.427 r_mcangle_it 1.084 r_mcbond_it 0.587 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.346 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 17.335 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.052 r_scbond_it 2.023 r_angle_refined_deg 1.427 r_mcangle_it 1.084 r_mcbond_it 0.587 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 14813 Nucleic Acid Atoms Solvent Atoms 981 Heterogen Atoms 216
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building ARP model building WARP model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing