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Crystal structure of HrmI in complex with the diferrous iron and N(6)-hydroxy-L-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 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.724 α = 90 b = 112.724 β = 90 c = 68.446 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 2025-05-30 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 2.05 39.77 99.3 0.083 0.094 0.044 0.994 5.4 4.3 31608
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 2.05 2.09 0.399 0.47 0.244 0.818 11.6 3.6
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 2.05 39.77 29994 1533 99.35 0.15845 0.15622 0.1712 0.20221 0.2118 RANDOM 26.937
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] 0.06 0.03 0.06 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.84 r_long_range_B_refined 7.675 r_long_range_B_other 7.487 r_dihedral_angle_2_deg 7.251 r_scangle_other 6.049 r_dihedral_angle_1_deg 5.75 r_scbond_it 3.983 r_scbond_other 3.982 r_mcangle_it 3.743 r_mcangle_other 3.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.84 r_long_range_B_refined 7.675 r_long_range_B_other 7.487 r_dihedral_angle_2_deg 7.251 r_scangle_other 6.049 r_dihedral_angle_1_deg 5.75 r_scbond_it 3.983 r_scbond_other 3.982 r_mcangle_it 3.743 r_mcangle_other 3.742 r_mcbond_it 2.727 r_mcbond_other 2.722 r_angle_refined_deg 1.892 r_angle_other_deg 0.673 r_chiral_restr 0.092 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 353 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction