☰ Navigation Tabs
Crystal structure of Frog M-ferritin E135K 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 62.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.12 α = 90 b = 184.12 β = 90 c = 184.12 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 1.73 21.26 99.9 19.2 12 29921
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 1.73 1.76 100 4.8 10.9
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 1.73 21.26 26925 1421 99.57 0.16478 0.16377 0.166 0.18297 0.182 RANDOM 17.226
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 39.243 r_dihedral_angle_4_deg 17.415 r_dihedral_angle_3_deg 14.486 r_long_range_B_refined 6.499 r_long_range_B_other 6.473 r_dihedral_angle_1_deg 5.138 r_scangle_other 4.971 r_scbond_it 3.823 r_scbond_other 3.822 r_mcangle_it 1.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.243 r_dihedral_angle_4_deg 17.415 r_dihedral_angle_3_deg 14.486 r_long_range_B_refined 6.499 r_long_range_B_other 6.473 r_dihedral_angle_1_deg 5.138 r_scangle_other 4.971 r_scbond_it 3.823 r_scbond_other 3.822 r_mcangle_it 1.873 r_mcangle_other 1.873 r_mcbond_other 1.43 r_mcbond_it 1.428 r_angle_refined_deg 1.08 r_angle_other_deg 0.647 r_chiral_restr 0.059 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 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 1433 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing