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Mutant (E53,56,57,60Q and R59M) recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V2L PDB ENTRY 2V2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 RESERVOIR: CADMIUM SULFATE 0.08M, AMMONIUM SULFATE 0.5M, SODIUM ACETATE 0.1M PH 5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 3.1 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.255 α = 90 b = 181.255 β = 90 c = 181.255 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 MARRESEARCH MIRROR 2 BENT, VERTICALLY FOCUSSING 2007-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.15 23 98.4 0.06 14 6.8 88729
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 1.15 1.2 87.8 0.46 3 3.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V2L 1.15 104.83 84284 4440 98.7 0.201 0.199 0.2113 0.224 RANDOM 11.58
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 37.935 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 11.437 r_scangle_it 5.836 r_dihedral_angle_1_deg 4.695 r_scbond_it 4.421 r_mcangle_it 2.593 r_mcbond_it 2.366 r_angle_refined_deg 1.666 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.935 r_dihedral_angle_4_deg 17.96 r_dihedral_angle_3_deg 11.437 r_scangle_it 5.836 r_dihedral_angle_1_deg 4.695 r_scbond_it 4.421 r_mcangle_it 2.593 r_mcbond_it 2.366 r_angle_refined_deg 1.666 r_angle_other_deg 0.981 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.262 r_symmetry_vdw_other 0.241 r_xyhbond_nbd_refined 0.22 r_nbd_other 0.204 r_nbtor_refined 0.19 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.105 r_nbtor_other 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1360 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling