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Mutant (E53,56,57,60Q and R59M) recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V2P PDB ENTRY 2V2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 RESERVOIR: CADMIUM SULFATE 0.16M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.2
Crystal Properties Matthews coefficient Solvent content 3.2 61.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.589 α = 90 b = 183.589 β = 90 c = 183.589 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 IMAGE PLATE MARRESEARCH MIRROR 1, FLAT PRE-MIRROR, MIRROR 2, BENT, VERTICALLY FOCUSSING 2006-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 20 98.9 0.09 14.9 6.9 21258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.9 0.53 4.2 7.1
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V2P 1.9 106 20161 1086 98.9 0.19 0.188 0.23 RANDOM 19.28
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 37.631 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 5.362 r_scangle_it 4.771 r_scbond_it 3.526 r_mcangle_it 1.814 r_mcbond_it 1.741 r_angle_refined_deg 1.633 r_angle_other_deg 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.631 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_1_deg 5.362 r_scangle_it 4.771 r_scbond_it 3.526 r_mcangle_it 1.814 r_mcbond_it 1.741 r_angle_refined_deg 1.633 r_angle_other_deg 1.08 r_symmetry_vdw_other 0.28 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.207 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.13 r_nbtor_other 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_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 1369 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling