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Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EQ6 PDB ENTRY 2EQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 45%(v/v) MPD, 200mM NaCl, 10mM NAD+, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.92 57.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.028 α = 90 b = 107.073 β = 90 c = 131.706 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 90 CCD ADSC QUANTUM 210 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPring-8 BL44B2
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 1.8 50 99.8 0.075 25.6 7.1 111571 14.6
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 1.8 1.86 99.6 0.413 3.6 6.6 10985
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 2EQ6 1.8 39.01 111470 5581 99.6 0.207 0.207 0.2021 0.238 0.2341 RANDOM 23.2
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] -4.04 -1.92 5.95
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.34 c_scbond_it 2.18 c_mcangle_it 1.75 c_angle_deg 1.2 c_mcbond_it 1.18 c_improper_angle_d 0.78 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.34 c_scbond_it 2.18 c_mcangle_it 1.75 c_angle_deg 1.2 c_mcbond_it 1.18 c_improper_angle_d 0.78 c_bond_d 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7130 Nucleic Acid Atoms Solvent Atoms 1159 Heterogen Atoms 194
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing