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Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate - W113A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AM3 8am3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 240 mM ammonium citrate tribasic
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.051 α = 90 b = 90.051 β = 90 c = 277.358 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2019-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.85 85.65 99.88 0.973 7 2.6 98195 20.861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.2 0.999 1.3
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 (All) 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 8am3 1.85 85.65 98192 4802 99.878 0.175 0.1731 0.1731 0.2154 0.2155 RANDOM 25.769
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] -0.002 -0.002 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.24 r_dihedral_angle_4_deg 19.599 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 6.902 r_lrange_it 4.858 r_scangle_it 4.003 r_scbond_it 2.791 r_mcangle_it 2.294 r_mcbond_it 1.682 r_angle_refined_deg 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.24 r_dihedral_angle_4_deg 19.599 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 6.902 r_lrange_it 4.858 r_scangle_it 4.003 r_scbond_it 2.791 r_mcangle_it 2.294 r_mcbond_it 1.682 r_angle_refined_deg 1.376 r_symmetry_nbd_refined 0.323 r_nbtor_refined 0.313 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.134 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.099 r_ncsr_local_group_1 0.062 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8173 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 197
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing SHELXDE phasing Coot model building CRANK phasing