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Molecular Genetic and Crystal Structural Analysis of 1-(4- Hydroxyphenyl)-Ethanol Dehydrogenase from Aromatoleum aromaticum EbN1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IY8 PDB ENTRY 1IY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP SITTING DROP METHOD IN A BUFFER CONTAINING 30% PEG 6000, 0.1 M NA-CACODYLATE (PH 6.5), 0.3 M MG-ACETATE
Crystal Properties Matthews coefficient Solvent content 1.97 37.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.5 α = 90 b = 55.1 β = 134.4 c = 86.3 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.4 31.76 91 0.05 12.87 2.5 73410
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 1.4 1.5 69 0.34 2.29 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IY8 1.4 31.76 69759 3672 91.42 0.13587 0.13241 0.20175 0.2154 RANDOM 20.192
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] -0.07 -0.08 -0.1 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_sphericity_free 29.264 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 13.16 r_sphericity_bonded 13.08 r_dihedral_angle_1_deg 6.475 r_rigid_bond_restr 5.153 r_scbond_it 4.739 r_mcangle_it 3.497 r_mcbond_it 3.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_sphericity_free 29.264 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 13.16 r_sphericity_bonded 13.08 r_dihedral_angle_1_deg 6.475 r_rigid_bond_restr 5.153 r_scbond_it 4.739 r_mcangle_it 3.497 r_mcbond_it 3.241 r_mcbond_other 3.238 r_angle_refined_deg 1.873 r_angle_other_deg 0.941 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3694 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing