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Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E6E PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 experimental model PDB 1AYF PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 experimental model PDB 1L6V PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 experimental model PDB 2BT6 PDB ENTRIES 1E6E,1AYF,1L6V,2BT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET.
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.965 α = 90 b = 81.965 β = 90 c = 68.289 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 IMAGE PLATE MAR scanner 345 mm plate 2004-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU H2B
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 2.6 20 99.5 0.11 8.5 3.4 8006 56.1
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 2.6 2.78 92.4 0.51 3.4 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 2.6 20 8006 390 99.5 0.184 0.182 0.187 0.235 0.244 RANDOM 45.15
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] 0.31 0.16 0.31 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.132 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 13.795 r_scangle_it 9.292 r_scbond_it 6.76 r_dihedral_angle_1_deg 5.593 r_mcangle_it 3.93 r_mcbond_it 3.23 r_angle_refined_deg 1.453 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.132 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 13.795 r_scangle_it 9.292 r_scbond_it 6.76 r_dihedral_angle_1_deg 5.593 r_mcangle_it 3.93 r_mcbond_it 3.23 r_angle_refined_deg 1.453 r_angle_other_deg 0.915 r_symmetry_vdw_other 0.31 r_nbd_refined 0.215 r_nbd_other 0.202 r_symmetry_vdw_refined 0.2 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.147 r_nbtor_other 0.09 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1567 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XSCALE data scaling SWISS-MODELLER phasing PHASER phasing REFMAC refinement