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Cytochrome cd1 Nitrite Reductase, x-ray reduced 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 DIOXYGEN SPECIES FORMED UNDER THESE CONDITIONS WAS REDUCED UPON X-RAY EXPOSURE AND THE RESULTING STRUCTURE REPRESENTS A MIXTURE OF STATES.
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.69 α = 90 b = 60.9 β = 112.08 c = 100.59 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 1998-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 93.9 0.041 0.041 14.2 2.2 149315 18.2
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 95.3 0.202 0.202 2.8
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 149315 93.9 0.202 0.226 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 29.3 p_special_tor 15 p_staggered_tor 10.9 p_planar_tor 4.2 p_multtor_nbd 0.24 p_singtor_nbd 0.18 p_xyhbond_nbd 0.152 p_chiral_restr 0.117 p_plane_restr 0.026 p_planar_d 0.024
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 29.3 p_special_tor 15 p_staggered_tor 10.9 p_planar_tor 4.2 p_multtor_nbd 0.24 p_singtor_nbd 0.18 p_xyhbond_nbd 0.152 p_chiral_restr 0.117 p_plane_restr 0.026 p_planar_d 0.024 p_angle_d 0.015 p_bond_d 0.013 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 8497 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling