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Mutant 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 2V2N PDB ENTRY 2V2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 RESERVOIR: CADMIUM SULFATE 0.145M, AMMONIUM SULFATE 0.55M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.2
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.801 α = 90 b = 183.801 β = 90 c = 183.801 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 1.87 21 99 0.07 25 7 22374
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 1.87 2 95.3 0.5 3.9 7
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V2N 1.87 106 21330 1147 99.5 0.198 0.196 0.236 0.2112 RANDOM 15.84
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 36.392 r_dihedral_angle_4_deg 23.441 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 5.496 r_scangle_it 4.203 r_scbond_it 3.105 r_angle_refined_deg 1.621 r_mcangle_it 1.61 r_mcbond_it 1.46 r_angle_other_deg 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.392 r_dihedral_angle_4_deg 23.441 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 5.496 r_scangle_it 4.203 r_scbond_it 3.105 r_angle_refined_deg 1.621 r_mcangle_it 1.61 r_mcbond_it 1.46 r_angle_other_deg 1.071 r_symmetry_vdw_other 0.273 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.231 r_nbd_other 0.188 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.107 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 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 1366 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling