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Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEV PDB ENTRY 1KEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.742 α = 90 b = 82.429 β = 99.89 c = 118.249 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 4 2003-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 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 1.4 50 99.3 0.075 20.143 3.1 294442 294442 -3 11.2
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 1.4 1.42 93 0.664 1.4 2.3 13706
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KEV 1.4 48.77 283136 293136 14820 99.14 0.118 0.118 0.116 0.1388 0.155 0.1698 RANDOM 15.204
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] -0.04 -0.5 -0.23 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.021 r_dihedral_angle_4_deg 15.24 r_dihedral_angle_3_deg 11.914 r_sphericity_free 6.795 r_dihedral_angle_1_deg 6.618 r_scangle_it 6.226 r_scbond_it 4.387 r_sphericity_bonded 3.41 r_mcangle_it 3.311 r_mcbond_it 2.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.021 r_dihedral_angle_4_deg 15.24 r_dihedral_angle_3_deg 11.914 r_sphericity_free 6.795 r_dihedral_angle_1_deg 6.618 r_scangle_it 6.226 r_scbond_it 4.387 r_sphericity_bonded 3.41 r_mcangle_it 3.311 r_mcbond_it 2.405 r_rigid_bond_restr 1.784 r_angle_refined_deg 1.507 r_mcbond_other 1.269 r_angle_other_deg 0.991 r_symmetry_vdw_other 0.233 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.218 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.176 r_metal_ion_refined 0.112 r_chiral_restr 0.103 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10675 Nucleic Acid Atoms Solvent Atoms 1988 Heterogen Atoms 97
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection