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Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 PEG 4000, Imidazol malate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.036 α = 90 b = 79.68 β = 95.77 c = 158.669 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 102 CCD ADSC QUANTUM 4 2002-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2
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 20 96.3 0.076 7.1 5.8 797404 116969 2 2
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 2.07 96.3 0.198
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.1 20 2 115545 6119 100 0.18588 0.18588 0.18445 0.1906 0.21309 0.2171 RANDOM 20.908
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] 0.29 0.48 0.08 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.761 r_scangle_it 3.935 r_dihedral_angle_1_deg 3.853 r_scbond_it 2.441 r_angle_refined_deg 1.49 r_mcangle_it 1.194 r_mcbond_it 0.588 r_symmetry_hbond_refined 0.35 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.761 r_scangle_it 3.935 r_dihedral_angle_1_deg 3.853 r_scbond_it 2.441 r_angle_refined_deg 1.49 r_mcangle_it 1.194 r_mcbond_it 0.588 r_symmetry_hbond_refined 0.35 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 14300 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing