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Crystal structure of Frog M-ferritin D40A 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 3.32 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.17 α = 90 b = 184.17 β = 90 c = 184.17 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++ 2016-01-11 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) 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 1.7 23.98 100 30.7 13 29984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 6.3 11.7
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 3KA3 1.7 23.98 28484 1461 99.89 0.15779 0.15631 0.1581 0.18735 0.1844 RANDOM 16.428
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 38.31 r_dihedral_angle_4_deg 15.018 r_dihedral_angle_3_deg 14.792 r_long_range_B_refined 6.17 r_long_range_B_other 6.021 r_dihedral_angle_1_deg 5.271 r_scangle_other 4.818 r_scbond_it 3.578 r_scbond_other 3.576 r_mcangle_other 1.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.31 r_dihedral_angle_4_deg 15.018 r_dihedral_angle_3_deg 14.792 r_long_range_B_refined 6.17 r_long_range_B_other 6.021 r_dihedral_angle_1_deg 5.271 r_scangle_other 4.818 r_scbond_it 3.578 r_scbond_other 3.576 r_mcangle_other 1.843 r_mcangle_it 1.842 r_mcbond_it 1.318 r_mcbond_other 1.309 r_angle_refined_deg 1.105 r_angle_other_deg 0.687 r_chiral_restr 0.067 r_gen_planes_refined 0.017 r_bond_refined_d 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1430 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing