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Crystal structure of HrmI in complex with the diferrous iron and lysine
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 291.15 HEPES, potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.75 α = 90 b = 112.75 β = 90 c = 68.487 γ = 120
Symmetry Space Group P 32 2 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 Bruker PHOTON II 2025-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.542
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 25.2 99.8 0.084 0.094 0.042 0.99 4.3 4.9 34210
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 2.03 0.42 0.487 0.244 0.816 9.9
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 (Observed) 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 2 25.2 32469 1688 99.85 0.15457 0.1528 0.1662 0.18872 0.1992 RANDOM 26.055
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] 0.07 0.03 0.07 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.975 r_long_range_B_refined 7.208 r_long_range_B_other 6.901 r_dihedral_angle_2_deg 6.417 r_scangle_other 5.849 r_dihedral_angle_1_deg 5.744 r_scbond_it 3.883 r_scbond_other 3.872 r_mcangle_other 3.464 r_mcangle_it 3.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.975 r_long_range_B_refined 7.208 r_long_range_B_other 6.901 r_dihedral_angle_2_deg 6.417 r_scangle_other 5.849 r_dihedral_angle_1_deg 5.744 r_scbond_it 3.883 r_scbond_other 3.872 r_mcangle_other 3.464 r_mcangle_it 3.438 r_mcbond_other 2.615 r_mcbond_it 2.614 r_angle_refined_deg 1.865 r_angle_other_deg 0.662 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2709 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction