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Crystal structure of the apo CYP123 from Mycobacterium smegmatis
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 M ammonium acetate, 0.1 M sodium citrate tribasic pH 5.6, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.314 α = 90 b = 132.314 β = 90 c = 126.835 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 2025-03-27 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 2.14 66.25 100 1 17.5 27.2 62580
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 2.14 2.2 1
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 2.14 66.245 62498 3239 99.984 0.222 0.2201 0.2264 0.2615 0.264 59.578
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] -0.142 -0.142 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.234 r_dihedral_angle_6_deg 13.045 r_lrange_it 6.928 r_lrange_other 6.922 r_dihedral_angle_2_deg 6.858 r_dihedral_angle_1_deg 6.7 r_scangle_it 5.282 r_scangle_other 5.281 r_mcangle_it 4.944 r_mcangle_other 4.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.234 r_dihedral_angle_6_deg 13.045 r_lrange_it 6.928 r_lrange_other 6.922 r_dihedral_angle_2_deg 6.858 r_dihedral_angle_1_deg 6.7 r_scangle_it 5.282 r_scangle_other 5.281 r_mcangle_it 4.944 r_mcangle_other 4.944 r_scbond_it 3.472 r_scbond_other 3.472 r_mcbond_it 3.371 r_mcbond_other 3.37 r_dihedral_angle_other_2_deg 1.283 r_angle_refined_deg 1.251 r_angle_other_deg 0.444 r_nbd_refined 0.217 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.159 r_nbd_other 0.156 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_refined 0.058 r_symmetry_xyhbond_nbd_other 0.012 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 186 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing