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Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O2D TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5.7 293 0.2M NaCl, 0.2% PEG-1000, 0.1M Na,K-Phosphate pH 5.7 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.691 α = 90 b = 129.699 β = 103.61 c = 55.234 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 2003-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.78 50 93.95 0.041 21.67 2.85 65785 36.93
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 1.78 1.84 68.72 0.338 1.94 1.87 4773
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 TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920) 1.78 49.6 62407 3343 93.86 0.14475 0.14224 0.1622 0.19265 0.1588 RANDOM 35.944
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] -0.38 1.73 -0.47 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_dihedral_angle_4_deg 15.307 r_dihedral_angle_3_deg 13.591 r_scangle_it 7.306 r_dihedral_angle_1_deg 5.671 r_scbond_it 5.538 r_mcangle_it 2.962 r_mcbond_it 2.249 r_angle_refined_deg 1.562 r_angle_other_deg 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.7 r_dihedral_angle_4_deg 15.307 r_dihedral_angle_3_deg 13.591 r_scangle_it 7.306 r_dihedral_angle_1_deg 5.671 r_scbond_it 5.538 r_mcangle_it 2.962 r_mcbond_it 2.249 r_angle_refined_deg 1.562 r_angle_other_deg 1 r_mcbond_other 0.617 r_symmetry_vdw_other 0.265 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.211 r_nbd_other 0.18 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.099 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.061 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6078 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 98
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing REFMAC refinement