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Crystal Structure of the apo form of Human H-Ferritin variant MIC1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CEI PDB ENTRY 2CEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 50 mM Tris, 10 mM calcium chloride, 4% PEG 400, soaked in 20 mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.066 α = 90 b = 181.066 β = 90 c = 181.066 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 CCD MARMOSAIC 325 mm CCD 2011-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.3 104.538 100 0.097 36.1 42 11848 11848 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.397 0.397 1.9 42.9 1680
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2CEI 2.3 90.54 11848 11847 819 99.97 0.2231 0.2194 0.2155 0.2715 0.269 RANDOM 25.9923
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 39.299 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 4.949 r_scangle_it 2.162 r_scbond_it 1.316 r_angle_refined_deg 0.996 r_mcangle_it 0.896 r_mcbond_it 0.541 r_nbtor_refined 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.299 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 4.949 r_scangle_it 2.162 r_scbond_it 1.316 r_angle_refined_deg 0.996 r_mcangle_it 0.896 r_mcbond_it 0.541 r_nbtor_refined 0.289 r_metal_ion_refined 0.246 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1413 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 5
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection