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Crystal structure of the Pyrococcus furiosus ferredoxin D14C variant containing the heterometallic [AgFe3S4] cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8Q PDB ENTRY 2Z8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 PEG600, malonic acid/imidazol/boric acid buffer mixture, [Co(NH3)6]Cl3, pH 7.5, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.11 α = 90 b = 49.33 β = 90 c = 54.39 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD 2011-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 1.95 25 94.5 0.077 7.63 3 16141
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 1.95 2.07 0.306 2.13 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2Z8Q 1.95 24.66 27000 9050 428 97.5 0.191 0.188 0.1882 0.247 0.2444 RANDOM 19.88
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.845 r_dihedral_angle_3_deg 15.526 r_dihedral_angle_1_deg 5.364 r_scangle_it 4.903 r_scbond_it 2.984 r_angle_refined_deg 1.7 r_mcangle_it 1.696 r_mcbond_it 0.942 r_chiral_restr 0.105 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.845 r_dihedral_angle_3_deg 15.526 r_dihedral_angle_1_deg 5.364 r_scangle_it 4.903 r_scbond_it 2.984 r_angle_refined_deg 1.7 r_mcangle_it 1.696 r_mcbond_it 0.942 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing