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Structure of the CYP102A1 Heme Domain with 2-(undecylcarbamoyl)benzoic acid
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 MgCl2
17% w/v PEG8000
0.5 mM 2-(undecylcarbamoyl)benzoic acid
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.083 α = 90 b = 129.482 β = 90 c = 149.598 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 1.63 46.4 100 0.193 0.997 11.6 13.3 143659 14.67
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 1.63 1.66 0.748
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 1.63 46.4 143557 7312 99.969 0.19 0.1883 0.1882 0.2159 0.2157 22.111
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] -0.071 0.516 -0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.197 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_2_deg 7.524 r_dihedral_angle_1_deg 6.811 r_lrange_it 5.923 r_lrange_other 5.893 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_other 3.268 r_mcangle_it 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.197 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_2_deg 7.524 r_dihedral_angle_1_deg 6.811 r_lrange_it 5.923 r_lrange_other 5.893 r_scangle_it 4.656 r_scangle_other 4.655 r_mcangle_other 3.268 r_mcangle_it 3.267 r_scbond_it 3.004 r_scbond_other 3.004 r_mcbond_it 2.246 r_mcbond_other 2.245 r_angle_refined_deg 1.897 r_dihedral_angle_other_2_deg 1.07 r_angle_other_deg 0.666 r_symmetry_nbd_refined 0.488 r_symmetry_xyhbond_nbd_refined 0.347 r_nbd_refined 0.236 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_other 0.15 r_nbd_other 0.141 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.076 r_metal_ion_refined 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 581 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing