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Crystal structure of Frog M-ferritin E130A_L165D mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 2.0 M MgCl2 and 100 mM Bicine (pH 9.0)
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.76 α = 90 b = 183.76 β = 90 c = 183.76 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 103 IMAGE PLATE RIGAKU RAXIS IV++ 2015-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.77 35.39 100 0.999 22 11 26270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 0.967
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KA3 1.77 35.39 25002 1268 99.9 0.157 0.1668 0.188 0.193 RANDOM 16.12
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_3_deg 15.144 r_scangle_other 6.113 r_scangle_it 6.105 r_dihedral_angle_1_deg 4.952 r_scbond_it 4.325 r_scbond_other 4.323 r_mcangle_it 3.023 r_mcangle_other 2.93 r_mcbond_other 2.027 r_mcbond_it 2.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.144 r_scangle_other 6.113 r_scangle_it 6.105 r_dihedral_angle_1_deg 4.952 r_scbond_it 4.325 r_scbond_other 4.323 r_mcangle_it 3.023 r_mcangle_other 2.93 r_mcbond_other 2.027 r_mcbond_it 2.025 r_angle_refined_deg 1.449 r_angle_other_deg 0.562 r_xyhbond_nbd_refined 0.369 r_nbd_refined 0.24 r_nbtor_refined 0.186 r_nbd_other 0.133 r_metal_ion_refined 0.131 r_symmetry_metal_ion_refined 0.094 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1429 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Coot model building MOSFLM data reduction Aimless data scaling MOLREP phasing