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Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 5 minutes under anaerobic environment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281.15 1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.14 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.675 α = 90 b = 183.675 β = 90 c = 183.675 γ = 90
Symmetry Space Group F 4 3 2
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 6M-F 2019-05-17 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-05-17 M MAD 3 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-05-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.90001 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.73892 Diamond I04 3 SYNCHROTRON DIAMOND BEAMLINE I04 1.75120 Diamond I04
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 1.4 106.04 100 0.067 0.07 0.015 1 26.3 22 52581 2 14.4
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 1.4 1.48 100 0.904 0.944 0.2 0.899 3.7 22.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1R03 1.4 106.04 49920 2638 100 0.1331 0.1315 0.1315 0.1625 0.1624 RANDOM 18.974
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_4_deg 15.026 r_dihedral_angle_3_deg 12.01 r_dihedral_angle_1_deg 5.238 r_rigid_bond_restr 2.446 r_angle_refined_deg 1.412 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1402 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing