☰ Navigation Tabs
Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 15 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 3.07 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.449 α = 90 b = 182.449 β = 90 c = 182.449 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 0.87000 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 1.2 55.01 100 0.066 0.07 0.015 1 22 20.1 81103 2 9.9
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 1.2 1.26 100 0.76 0.817 0.215 0.869 3.3 14.1
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 1.2 52.72 76990 4101 99.97 0.1222 0.1212 0.1212 0.1425 0.1426 RANDOM 13.691
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 38.35 r_dihedral_angle_4_deg 12.358 r_dihedral_angle_3_deg 12.119 r_dihedral_angle_1_deg 5.34 r_rigid_bond_restr 1.684 r_angle_other_deg 1.591 r_angle_refined_deg 1.469 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.35 r_dihedral_angle_4_deg 12.358 r_dihedral_angle_3_deg 12.119 r_dihedral_angle_1_deg 5.34 r_rigid_bond_restr 1.684 r_angle_other_deg 1.591 r_angle_refined_deg 1.469 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1403 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing