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Cytochrome cd1 Nitrite Reductase, dioxygen complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AOF PDB ENTRY 1AOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 2.3 M AMMONIUM SULFATE 50MM POTASSIUM PHOSPHATE PH 7.0 CRYSTALS WERE REDUCED USING 20MM SODIUM DITHIONITE. THE CRYSTAL WAS TRANSFERRED TO A SOLUTION CONTAINING 2.3 M AMMONIUM SULFATE, 50 MM PHOSPAHTE BUFFER PH 7 AND 15 % GLYCEROL. O2 WAS INTRODUCED UNDER 15 ATM PRESSURE FOR 2 MINUTES AT -20 DEGREES. THE DATA SET IS COMPOSED 10 DEGREE WEDGES OF DATA FROM 11 IDENTICAL CRYSTALS.
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.19 α = 90 b = 61.17 β = 112.19 c = 100.52 γ = 90
Symmetry Space Group P 1 21 1
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 1999-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 30 85.3 0.046 0.046 14.1 2.1 135637 17.714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 85.4 0.175 0.175 2.9
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AOF 1.6 30 135637 85.3 0.196 0.219 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 29.4 p_special_tor 15 p_staggered_tor 11.2 p_planar_tor 4.5 p_multtor_nbd 0.241 p_singtor_nbd 0.179 p_xyhbond_nbd 0.149 p_chiral_restr 0.127 p_plane_restr 0.024 p_planar_d 0.018
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 29.4 p_special_tor 15 p_staggered_tor 11.2 p_planar_tor 4.5 p_multtor_nbd 0.241 p_singtor_nbd 0.179 p_xyhbond_nbd 0.149 p_chiral_restr 0.127 p_plane_restr 0.024 p_planar_d 0.018 p_bond_d 0.014 p_angle_d 0.014 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_xhyhbond_nbd p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8445 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling