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Crystal structure of the diheme 4D2 (mutant T19D) with bound Fe(III) 2,4-diformyl deuteroporphyrin IX
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 293 Protein Buffer 20 mM CHES, 100 mM KCl, pH 8.6. Crystallisation condition 2.1M DL-Malic Acid, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.06 59.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.271 α = 90 b = 81.271 β = 90 c = 60.967 γ = 120
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 XE 16M 2025-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.997 46.082 100 0.033 0.999 11.8 10.7 10188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.997 2.032 100 0.744 0.516 9.2
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 THROUGHOUT 1.998 46.082 10158 503 99.735 0.185 0.1824 0.1853 0.2286 0.2305 RANDOM 45.76
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] -2.185 -1.093 -2.185 7.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.072 r_dihedral_angle_3_deg 14.594 r_lrange_it 10.351 r_scangle_it 8.878 r_dihedral_angle_2_deg 7.541 r_scbond_it 6.122 r_mcangle_it 5.889 r_dihedral_angle_1_deg 4.756 r_mcbond_it 4.142 r_angle_refined_deg 1.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.072 r_dihedral_angle_3_deg 14.594 r_lrange_it 10.351 r_scangle_it 8.878 r_dihedral_angle_2_deg 7.541 r_scbond_it 6.122 r_mcangle_it 5.889 r_dihedral_angle_1_deg 4.756 r_mcbond_it 4.142 r_angle_refined_deg 1.882 r_nbtor_refined 0.29 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.106 r_symmetry_xyhbond_nbd_refined 0.105 r_metal_ion_refined 0.051 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 840 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement autoPROC data processing MOLREP phasing autoPROC data reduction autoPROC data scaling