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Crystal Structure of the Zn-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JD6 PDB ENTRY 2JD6
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 MICROL ITERS OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION. ZINC SOAKING OF FERRITIN CRYSTALS WAS PERFORMED BY TRANSFERRING THEM TO A 10-20 MICROLITER DROP OF A SOLUTION WITH COMPOSITION 20 MM ZNCL2, 25 % GLYCEROL AND 2 M AMMONIUM SULFATE, FOR 15 MINUTES.
Crystal Properties Matthews coefficient Solvent content 4 69.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 255.371 α = 90 b = 342.055 β = 90 c = 265.986 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 COLLIMATING AND FOCUSSING MIRRORS 2006-06-25 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 2.8 42.9 98.7 0.08 8.8 3.9 279537 58.5
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 2.8 2.95 91.6 0.29 2.5 3
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 2JD6 2.8 204.12 265356 14134 98.7 0.203 0.2 0.251 RANDOM 32.53
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] 1.31 -0.65 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.101 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_4_deg 16.5 r_scangle_it 6.988 r_dihedral_angle_1_deg 5.603 r_scbond_it 4.705 r_mcangle_it 3.32 r_mcbond_it 2.03 r_angle_refined_deg 1.479 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.101 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_4_deg 16.5 r_scangle_it 6.988 r_dihedral_angle_1_deg 5.603 r_scbond_it 4.705 r_mcangle_it 3.32 r_mcbond_it 2.03 r_angle_refined_deg 1.479 r_nbtor_refined 0.322 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.102 r_bond_refined_d 0.015 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 162 Heterogen Atoms 328
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling