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Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate cyclohex-2-en-1-one - inactive mutant (Y195F)
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 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.03 α = 90 b = 121.7 β = 90 c = 158.15 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.33 60.932 99.9 0.15 1 8.3 7.5 290848
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 1.33 1.35 0.6 1.1
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-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 8am3 1.33 60.932 290724 14422 99.863 0.175 0.175 0.174 0.174 0.1947 0.1947 RANDOM 17.368
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 28.42 r_dihedral_angle_4_deg 19.573 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.683 r_lrange_it 5.251 r_scangle_it 3.649 r_scbond_it 2.617 r_angle_refined_deg 1.789 r_mcangle_it 1.781 r_mcbond_it 1.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.42 r_dihedral_angle_4_deg 19.573 r_dihedral_angle_3_deg 11.352 r_dihedral_angle_1_deg 6.683 r_lrange_it 5.251 r_scangle_it 3.649 r_scbond_it 2.617 r_angle_refined_deg 1.789 r_mcangle_it 1.781 r_mcbond_it 1.261 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.147 r_chiral_restr 0.117 r_ncsr_local_group_1 0.051 r_gen_planes_refined 0.014 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8264 Nucleic Acid Atoms Solvent Atoms 1292 Heterogen Atoms 369
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing SHELXDE phasing Coot model building CRANK phasing