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X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 100 mM Tris, 200 mM Li2SO4, 30% PEG 4000, Anaerobic chamber (N2/H2 95/5%)
, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.132 α = 90 b = 78.729 β = 90 c = 86.209 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 ADSC QUANTUM 210 2005-06-21
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 60 85.4 119182 101819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54 88.06
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 (All) 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 3CIW 1.5 58.12 52356 52356 2809 98.14 0.12363 0.12363 0.1214 0.1232 0.16553 0.166 RANDOM 10.767
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] 0.5 -0.09 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.576 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_1_deg 11.831 r_dihedral_angle_3_deg 11.722 r_sphericity_free 10.043 r_scangle_it 4.028 r_sphericity_bonded 3.847 r_mcangle_it 3.107 r_scbond_it 2.956 r_mcbond_it 2.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.576 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_1_deg 11.831 r_dihedral_angle_3_deg 11.722 r_sphericity_free 10.043 r_scangle_it 4.028 r_sphericity_bonded 3.847 r_mcangle_it 3.107 r_scbond_it 2.956 r_mcbond_it 2.357 r_rigid_bond_restr 1.826 r_angle_refined_deg 1.74 r_mcbond_other 1.197 r_angle_other_deg 1.01 r_chiral_restr 0.112 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2726 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 206
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling