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Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CJE PDB ENTRY 1CJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293.15 1.75M Potassium Citrate (K3Cit), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.4 63.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.576 α = 90 b = 76.576 β = 90 c = 234.41 γ = 120
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 315 Kirkpatrick Baez bimorph mirror pair 2009-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 2.54 50.5 99.8 0.111 11.6 5.8 50847 50786 53.4
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) 2.54 2.67 99 0.721 2 3.9 7351
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB ENTRY 1CJE 2.54 43.91 2 50786 48817 1971 99.74 0.20541 0.20541 0.20395 0.2052 0.24132 0.2383 RANDOM 39.327
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] -1.08 -0.54 -1.08 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 14.765 r_sphericity_free 9.033 r_dihedral_angle_1_deg 5.923 r_scangle_it 2.194 r_scbond_it 2.002 r_angle_refined_deg 1.486 r_angle_other_deg 0.93 r_mcangle_it 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 14.765 r_sphericity_free 9.033 r_dihedral_angle_1_deg 5.923 r_scangle_it 2.194 r_scbond_it 2.002 r_angle_refined_deg 1.486 r_angle_other_deg 0.93 r_mcangle_it 0.786 r_mcbond_it 0.421 r_mcbond_other 0.11 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7733 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 169
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling