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Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin
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 6.5 293 0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.274 α = 90 b = 65.357 β = 107.793 c = 74.779 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 PILATUS3 X 6M 2025-10-15 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) 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 1.51 47.1 99 0.24 0.26 0.098 0.994 6.7 6.9 101480 9.56
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 1.51 1.54 98.7 2.013 2.171 0.808 0.636 1.3 7.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.51 47.1 101456 4988 98.859 0.203 0.2014 0.1961 0.234 0.229 13.434
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] -0.73 -0.57 2.714 -1.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.051 r_dihedral_angle_6_deg 14.988 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_1_deg 6.65 r_lrange_it 4.474 r_lrange_other 4.375 r_scangle_it 3.226 r_scangle_other 3.225 r_scbond_it 2.126 r_scbond_other 2.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.051 r_dihedral_angle_6_deg 14.988 r_dihedral_angle_3_deg 11.281 r_dihedral_angle_1_deg 6.65 r_lrange_it 4.474 r_lrange_other 4.375 r_scangle_it 3.226 r_scangle_other 3.225 r_scbond_it 2.126 r_scbond_other 2.126 r_mcangle_it 1.871 r_mcangle_other 1.871 r_angle_refined_deg 1.599 r_mcbond_it 1.214 r_mcbond_other 1.211 r_angle_other_deg 0.565 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.225 r_symmetry_nbd_other 0.206 r_nbd_other 0.198 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_other 0.152 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_metal_ion_refined 0.121 r_metal_ion_refined 0.108 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.083 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5090 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing