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Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M Ammonium iodide
20 % w/v PEG 3350
1 mM Cyanide
5 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.64 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.429 α = 90 b = 129.3 β = 106.048 c = 78.651 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 4M 2025-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 65.254 98.51 0.3247 0.3498 0.129 0.986 6.92 7.2 76424 36.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.268 96.78 2.636 2.832 1.028 0.405 1.16 7.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.194 65.254 76213 1754 97.965 0.183 0.1804 0.1891 0.2061 0.2203 RANDOM 44.79
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] -12.214 -16.548 35.142 -22.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.877 r_dihedral_angle_6_deg 14.596 r_lrange_it 10.392 r_dihedral_angle_2_deg 9.74 r_scangle_it 8.79 r_dihedral_angle_1_deg 7.087 r_scbond_it 6.984 r_mcangle_it 6.869 r_mcbond_it 5.639 r_angle_refined_deg 1.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.877 r_dihedral_angle_6_deg 14.596 r_lrange_it 10.392 r_dihedral_angle_2_deg 9.74 r_scangle_it 8.79 r_dihedral_angle_1_deg 7.087 r_scbond_it 6.984 r_mcangle_it 6.869 r_mcbond_it 5.639 r_angle_refined_deg 1.997 r_symmetry_nbd_refined 0.336 r_nbtor_refined 0.311 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.216 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.136 r_ncsr_local_group_3 0.1 r_ncsr_local_group_8 0.097 r_ncsr_local_group_9 0.091 r_ncsr_local_group_2 0.088 r_ncsr_local_group_6 0.088 r_ncsr_local_group_1 0.085 r_ncsr_local_group_7 0.084 r_ncsr_local_group_4 0.081 r_ncsr_local_group_10 0.081 r_ncsr_local_group_5 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10046 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction PHASER phasing Coot model building