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Cytochrome P450 decarboxylase from Staphylococcus aureus (OleT_Sa) with elaidic acid and acetate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2.8 M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 3.27 62.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.786 α = 90 b = 137.786 β = 90 c = 59.214 γ = 120
Symmetry Space Group P 32 2 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 X 16M 2024-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 1.83 53.04 99.9 0.24 0.99 14.7 82 101189 28.2
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 1.83 1.86 0.38 0.41
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.83 53.04 54096 3006 99.99 0.1654 0.16382 0.19415 0.2009 RANDOM 41.807
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] -2.19 -1.09 -2.19 7.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.884 r_dihedral_angle_2_deg 8.867 r_long_range_B_refined 7.19 r_long_range_B_other 7.173 r_dihedral_angle_1_deg 6.514 r_scangle_other 6.152 r_scbond_it 4.45 r_scbond_other 4.423 r_mcangle_it 3.184 r_mcangle_other 3.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.884 r_dihedral_angle_2_deg 8.867 r_long_range_B_refined 7.19 r_long_range_B_other 7.173 r_dihedral_angle_1_deg 6.514 r_scangle_other 6.152 r_scbond_it 4.45 r_scbond_other 4.423 r_mcangle_it 3.184 r_mcangle_other 3.184 r_mcbond_it 2.626 r_mcbond_other 2.613 r_angle_refined_deg 2.427 r_angle_other_deg 0.812 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3482 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling