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Crystal structure of Frog M-ferritin E130A_M161Q_L165D_K168E_H169D 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 277 2.0 M MgCl2 and 100 mM Bicine (pH 9.0)
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.95 α = 90 b = 183.95 β = 90 c = 183.95 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 CCD MARMOSAIC 225 mm CCD 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 1.55 46.03 100 0.998 29.2 13.4 39193
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 1.55 1.58 0.989
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 1.55 46.03 37227 1966 99.9 0.127 0.1473 0.153 0.168 RANDOM 14.2
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 14.965 r_scangle_it 10.863 r_scangle_other 10.787 r_mcangle_it 7.69 r_scbond_other 7.69 r_scbond_it 7.687 r_mcangle_other 7.631 r_mcbond_it 5.391 r_mcbond_other 5.289 r_dihedral_angle_1_deg 4.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.965 r_scangle_it 10.863 r_scangle_other 10.787 r_mcangle_it 7.69 r_scbond_other 7.69 r_scbond_it 7.687 r_mcangle_other 7.631 r_mcbond_it 5.391 r_mcbond_other 5.289 r_dihedral_angle_1_deg 4.871 r_rigid_bond_restr 2.563 r_angle_refined_deg 1.44 r_angle_other_deg 0.572 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.237 r_nbtor_refined 0.191 r_nbd_other 0.131 r_metal_ion_refined 0.075 r_chiral_restr 0.068 r_bond_refined_d 0.011 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_refined r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1428 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Coot model building iMOSFLM data reduction Aimless data scaling MOLREP phasing