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Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFX PDB ENTRY 1DFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 18% PEG 4000, 100 MM TRIS PH 8.0, 100 MM CACL2
Crystal Properties Matthews coefficient Solvent content 2.07 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.13 α = 90 b = 67.65 β = 90 c = 82.19 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 CCD MIRRORS 2003-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.69 37.49 97.8 0.09 11.7 2.9 26101 2 18.2
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 1DFX 1.69 37.49 25836 1285 96.4 0.207 0.207 0.2017 0.25 0.242 RANDOM 18.9
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] 0.56 -0.34 -0.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_improper_angle_d 4.77 c_scangle_it 3.02 c_scbond_it 2.07 c_mcangle_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.29 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_improper_angle_d 4.77 c_scangle_it 3.02 c_scbond_it 2.07 c_mcangle_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.29 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1956 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 31
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling CNS phasing