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Structure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 291 0.1 M Tris (base)-Bicine pH 8.25; 20% (v/v) PEG 500*MME; 10% (w/v) PEG 20000; 0.2 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D- Glucosamine)
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.184 α = 90 b = 53.052 β = 96.975 c = 101.643 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 PIXEL DECTRIS EIGER2 S 9M 2023-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.52 100.891 99.6 0.1771 0.968 6.29 6.2 18944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.61 99.79 1.202 0.29
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 AlphaFold2 2.52 100.891 18913 912 99.889 0.223 0.2177 0.2265 0.3216 0.3279 RANDOM 49.958
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] 1.155 -2.009 -0.693 0.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_6_deg 14.083 r_lrange_it 12.688 r_lrange_other 12.632 r_dihedral_angle_1_deg 7.389 r_dihedral_angle_2_deg 6.576 r_scangle_it 6.507 r_scangle_other 6.506 r_mcangle_it 6.18 r_mcangle_other 6.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_6_deg 14.083 r_lrange_it 12.688 r_lrange_other 12.632 r_dihedral_angle_1_deg 7.389 r_dihedral_angle_2_deg 6.576 r_scangle_it 6.507 r_scangle_other 6.506 r_mcangle_it 6.18 r_mcangle_other 6.179 r_scbond_it 4.059 r_scbond_other 4.058 r_mcbond_it 3.952 r_mcbond_other 3.951 r_angle_refined_deg 1.486 r_angle_other_deg 0.504 r_nbd_refined 0.231 r_symmetry_nbd_other 0.211 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.182 r_nbd_other 0.175 r_symmetry_nbd_refined 0.161 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4049 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing