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Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PED PDB ENTRY 1PED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 298 Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ammonium acetate, 15% (w/v) PEG 4000, 25mM NaCl, 50mM DTT, 25mM ZnCl2 and 50mM tri-citrate dihydrate (pH sodium 5.6), Microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.477 α = 90 b = 129.477 β = 90 c = 129.477 γ = 90
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 1.9 91.67 99.8 0.068 30.2 12 28452 -3 17.4
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 1.9 1.95 99.8 0.44 2.2 12 2004
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 1PED 1.9 19.98 28452 1437 99.81 0.125 0.122 0.1337 0.172 0.1766 RANDOM 24.753
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_4_deg 17.557 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.863 r_scangle_it 5.579 r_scbond_it 4.497 r_mcangle_it 2.542 r_mcbond_it 2.142 r_angle_refined_deg 1.553 r_angle_other_deg 0.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_4_deg 17.557 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.863 r_scangle_it 5.579 r_scbond_it 4.497 r_mcangle_it 2.542 r_mcbond_it 2.142 r_angle_refined_deg 1.553 r_angle_other_deg 0.998 r_mcbond_other 0.567 r_symmetry_vdw_other 0.376 r_symmetry_vdw_refined 0.256 r_xyhbond_nbd_refined 0.231 r_nbd_refined 0.216 r_nbd_other 0.202 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.098 r_nbtor_other 0.087 r_metal_ion_refined 0.029 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2635 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 22
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection HKL-2000 data reduction SCALEPACK data scaling