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Frog M-ferritin with cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KA3 PDB entry 3KA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 2M MgCl2, 0.1M Bicine pH 9.0, 0.1M CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.765 α = 90 b = 183.765 β = 90 c = 183.765 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 ADSC QUANTUM 315r Mirror 1: plane parabola Pt and Rh-coated Invar steel. Mirror 2: torroid Pt and Rh-coated Si M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
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 1.4 50 100 0.089 23.5 15 52653 52634
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 PDB entry 3KA3 1.4 50 52633 2685 99.98 0.149 0.147 0.1495 0.174 0.1744 RANDOM 15.513
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 37.971 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 14.385 r_sphericity_free 11.784 r_scangle_it 6.461 r_dihedral_angle_1_deg 4.799 r_scbond_it 4.641 r_sphericity_bonded 3.897 r_mcangle_it 2.74 r_rigid_bond_restr 2.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 14.385 r_sphericity_free 11.784 r_scangle_it 6.461 r_dihedral_angle_1_deg 4.799 r_scbond_it 4.641 r_sphericity_bonded 3.897 r_mcangle_it 2.74 r_rigid_bond_restr 2.168 r_angle_refined_deg 2.021 r_mcbond_it 1.948 r_angle_other_deg 1.692 r_mcbond_other 0.81 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1418 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 22
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling