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Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 3 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 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.09 α = 90 b = 184.09 β = 90 c = 184.09 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 1.47 29.11 100 0.108 0.113 0.024 0.999 14.6 21.9 45819 2 15.7
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 1.47 1.55 100 0.671 0.702 0.151 0.932 4.2 21.4
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 1.47 28.09 43580 2229 99.94 0.1466 0.146 0.1461 0.1571 0.1566 RANDOM 19.047
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 38.5 r_dihedral_angle_4_deg 12.924 r_dihedral_angle_3_deg 12.384 r_dihedral_angle_1_deg 5.058 r_angle_refined_deg 1.367 r_chiral_restr 0.093 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1406 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing