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Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter sphaeroides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWF pdb entry 2NWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 278 1.5 M Ammonium sulfate, 20% anhydrous glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.568 α = 90 b = 70.568 β = 90 c = 54.769 γ = 90
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.2 12 98 0.02 24.7 4.2 41254 41254 2 2
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 1.24 99.7 0.065 19.6 4.2 4192
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 entry 2NWF 1.2 11.67 38022 3177 98.16 0.11969 0.11828 0.1187 0.13639 0.1362 RANDOM 9.781
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] -0.02 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.503 r_sphericity_free 21.201 r_dihedral_angle_4_deg 11.87 r_dihedral_angle_3_deg 8.532 r_dihedral_angle_1_deg 5.089 r_sphericity_bonded 2.547 r_scangle_it 1.869 r_angle_refined_deg 1.738 r_mcangle_it 1.513 r_scbond_it 1.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.503 r_sphericity_free 21.201 r_dihedral_angle_4_deg 11.87 r_dihedral_angle_3_deg 8.532 r_dihedral_angle_1_deg 5.089 r_sphericity_bonded 2.547 r_scangle_it 1.869 r_angle_refined_deg 1.738 r_mcangle_it 1.513 r_scbond_it 1.363 r_mcbond_it 1.145 r_angle_other_deg 0.953 r_rigid_bond_restr 0.747 r_mcbond_other 0.533 r_symmetry_vdw_refined 0.302 r_nbd_refined 0.231 r_nbd_other 0.192 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.126 r_symmetry_vdw_other 0.122 r_chiral_restr 0.09 r_nbtor_other 0.083 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2153 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing