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Crystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine bifunctional chelator (DFO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.8 293 2.4 M (NH4)2SO4, 0.23 M (NH4)2HPO4, 0.07 M (NH4)H2PO4
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.807 α = 90 b = 62.863 β = 90 c = 153.594 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2M 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.55 76.8 94.2 25.9 4 139941
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 78 0.55 0.87 2.01 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3P5Q 1.55 48.69 2 70661 3620 95.48 0.16882 0.16663 0.1709 0.21178 0.216 RANDOM 30.158
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] -1 1.72 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 20.225 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_1_deg 16.01 r_long_range_B_refined 6.553 r_long_range_B_other 6.433 r_angle_refined_deg 1.744 r_scangle_other 1.71 r_angle_other_deg 1.473 r_mcangle_it 1.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 20.225 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_1_deg 16.01 r_long_range_B_refined 6.553 r_long_range_B_other 6.433 r_angle_refined_deg 1.744 r_scangle_other 1.71 r_angle_other_deg 1.473 r_mcangle_it 1.429 r_mcangle_other 1.429 r_scbond_it 1.148 r_scbond_other 1.104 r_mcbond_it 0.892 r_mcbond_other 0.891 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.001 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 4384 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing