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Crystal Structure of the as isolated Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VLG PDB ENTRY 1VLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 4 69.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.097 α = 90 b = 341.422 β = 90 c = 265.524 γ = 90
Symmetry Space Group C 2 2 21
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 2005-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.75 58.2 99.7 0.08 16.5 5.7 295335
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 2.75 2.9 97.8 0.3 3.1 3.6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VLG 2.75 204.12 280375 14914 99.6 0.198 0.195 0.247 RANDOM 33.98
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] 1.91 -0.92 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.842 r_dihedral_angle_3_deg 18.611 r_dihedral_angle_4_deg 15.328 r_scangle_it 7.098 r_dihedral_angle_1_deg 5.337 r_scbond_it 4.778 r_mcangle_it 3.252 r_mcbond_it 2.074 r_angle_refined_deg 1.432 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.842 r_dihedral_angle_3_deg 18.611 r_dihedral_angle_4_deg 15.328 r_scangle_it 7.098 r_dihedral_angle_1_deg 5.337 r_scbond_it 4.778 r_mcangle_it 3.252 r_mcbond_it 2.074 r_angle_refined_deg 1.432 r_nbtor_refined 0.321 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.099 r_bond_refined_d 0.014 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_refined r_metal_ion_other r_symmetry_vdw_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 49788 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing