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Structure of the CYP102A1 Heme Domain with 2-(undecylcarbamoyl)benzoic acid and benzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 100 mM Tris-HCl, 120 mM magnesium chloride, 18% w/v PEG8000, 0.5 mM 2-(undecylcarbamoyl)benzoic acid
Crystals were soaked in cryobuffer containing benzene.
Crystal Properties Matthews coefficient Solvent content 2.7 54.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.714 α = 90 b = 128.606 β = 90 c = 148.894 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 PILATUS3 X 6M 2025-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
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 1.48 46.1 100 0.291 0.996 11.7 13.1 187855 9.52
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 1.48 1.51 0.823
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6K58 1.48 46.1 187753 9377 99.928 0.178 0.1765 0.1738 0.199 0.1964 15.024
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] -0.084 0.436 -0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.145 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_2_deg 7.866 r_dihedral_angle_1_deg 6.336 r_lrange_it 5.05 r_lrange_other 4.952 r_scangle_it 4.164 r_scangle_other 4.163 r_scbond_it 2.683 r_scbond_other 2.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.145 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_2_deg 7.866 r_dihedral_angle_1_deg 6.336 r_lrange_it 5.05 r_lrange_other 4.952 r_scangle_it 4.164 r_scangle_other 4.163 r_scbond_it 2.683 r_scbond_other 2.683 r_mcangle_other 2.271 r_mcangle_it 2.27 r_angle_refined_deg 1.984 r_mcbond_it 1.532 r_mcbond_other 1.532 r_dihedral_angle_other_2_deg 1.108 r_angle_other_deg 0.677 r_nbd_refined 0.232 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.185 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.103 r_chiral_restr 0.102 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 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 7342 Nucleic Acid Atoms Solvent Atoms 816 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement X-Area data reduction Aimless data scaling MOLREP phasing