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Horse spleen Apoferritin 1.33 MGy variable temperature dose series, 140 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 20 mg/ml protein, 0.6M (NH4)SO4, 10 mM CdSO4
Cryoprotection buffer was the mother liquor with 40% of the water replaced by glycerol
Crystal Properties Matthews coefficient Solvent content 3.14 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.565 α = 90 b = 181.565 β = 90 c = 181.565 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 140 CCD ADSC QUANTUM 315 2004-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9764 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.15 104.83 100 0.08 24.7 7.7 13784 23.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 0.36 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.15 104.83 13784 730 99.9 0.19219 0.19102 0.187 0.21485 0.2091 RANDOM 20.878
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 35.452 r_dihedral_angle_4_deg 22.093 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_1_deg 6.091 r_scangle_it 5.382 r_scbond_it 3.435 r_mcangle_it 2.026 r_angle_refined_deg 1.653 r_mcbond_it 1.323 r_symmetry_metal_ion_refined 0.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.452 r_dihedral_angle_4_deg 22.093 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_1_deg 6.091 r_scangle_it 5.382 r_scbond_it 3.435 r_mcangle_it 2.026 r_angle_refined_deg 1.653 r_mcbond_it 1.323 r_symmetry_metal_ion_refined 0.488 r_metal_ion_refined 0.414 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.142 r_xyhbond_nbd_refined 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other 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 1398 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction REFMAC phasing PDB_EXTRACT data extraction