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Mutant R59M recombinant horse spleen apoferritin crystallized in acidic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V2N PDB ENTRY 2V2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 1.1M, SODIUM ACETATE 0.1M PH5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.1 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.242 α = 90 b = 181.242 β = 90 c = 181.242 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 1.37 23 99.9 0.1 15 10.9 53821
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 1.37 1.5 98.8 0.56 4.2 10.2
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 2V2N 1.37 104.83 51086 2735 99.9 0.203 0.202 0.2108 0.226 RANDOM 13.32
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 37.722 r_dihedral_angle_4_deg 21.343 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 5.015 r_scangle_it 4.964 r_scbond_it 3.581 r_mcangle_it 1.816 r_mcbond_it 1.746 r_angle_refined_deg 1.708 r_angle_other_deg 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.722 r_dihedral_angle_4_deg 21.343 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 5.015 r_scangle_it 4.964 r_scbond_it 3.581 r_mcangle_it 1.816 r_mcbond_it 1.746 r_angle_refined_deg 1.708 r_angle_other_deg 1.097 r_symmetry_vdw_refined 0.38 r_symmetry_vdw_other 0.28 r_nbd_refined 0.261 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.203 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.182 r_chiral_restr 0.128 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 1366 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling