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X-ray structure of CYP123 from Mycobacterium smegmatis with bound polyethylene glycol (PEG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-I7G922-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 mM ammonium acetate, 0.1 mM sodium citrate tribasic pH 5.6, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.14 60.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.904 α = 90 b = 132.904 β = 90 c = 127.215 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 EIGER2 X 16M 2024-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.19 66.54 100 0.999 13.8 27.3 59134
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 2.19 2.25 0.584
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.19 66.54 59056 3072 99.98 0.213 0.2102 0.2162 0.2719 0.2769 55.503
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] 0.159 0.159 -0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.268 r_dihedral_angle_6_deg 14.484 r_dihedral_angle_2_deg 9.615 r_lrange_it 8.434 r_lrange_other 8.433 r_dihedral_angle_1_deg 6.975 r_scangle_it 6.857 r_scangle_other 6.856 r_mcangle_other 6.305 r_mcangle_it 6.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.268 r_dihedral_angle_6_deg 14.484 r_dihedral_angle_2_deg 9.615 r_lrange_it 8.434 r_lrange_other 8.433 r_dihedral_angle_1_deg 6.975 r_scangle_it 6.857 r_scangle_other 6.856 r_mcangle_other 6.305 r_mcangle_it 6.304 r_scbond_it 4.874 r_scbond_other 4.873 r_mcbond_it 4.575 r_mcbond_other 4.569 r_angle_refined_deg 1.671 r_dihedral_angle_other_2_deg 1.641 r_angle_other_deg 0.572 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.156 r_nbd_other 0.153 r_metal_ion_refined 0.092 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6289 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing