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Wild type 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 2V2I PDB ENTRY 2V2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 RESERVOIR: CADMIUM SULFATE 0.04M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M DROP: 1UL PROTEIN AND 1 UL RESERVOIR, pH 8.2
Crystal Properties Matthews coefficient Solvent content 3.2 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.981 α = 90 b = 182.981 β = 90 c = 182.981 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 MIRRORS 2004-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18
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 2.22 29 98.3 0.04 25.7 4.2 13290
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 2.22 2.3 97.8 0.14 9.3 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V2I 2.22 105.41 12639 650 98.4 0.189 0.186 0.1885 0.25 0.2522 RANDOM 18.12
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 36.739 r_dihedral_angle_4_deg 20.658 r_dihedral_angle_3_deg 15.013 r_dihedral_angle_1_deg 5.745 r_scangle_it 4.282 r_scbond_it 3.09 r_angle_refined_deg 1.632 r_mcangle_it 1.557 r_mcbond_it 1.433 r_angle_other_deg 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.739 r_dihedral_angle_4_deg 20.658 r_dihedral_angle_3_deg 15.013 r_dihedral_angle_1_deg 5.745 r_scangle_it 4.282 r_scbond_it 3.09 r_angle_refined_deg 1.632 r_mcangle_it 1.557 r_mcbond_it 1.433 r_angle_other_deg 1.023 r_nbd_refined 0.233 r_symmetry_vdw_other 0.215 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.097 r_nbtor_other 0.092 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 1363 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling