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Cytochrome cd1 Nitrite Reductase, reoxidised enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QKS PDB ENTRY 1QKS
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 60 MINUTES AT -20 DEGREES. UNDER THESE CONDITIONS THE ENZYME UNDERGO A COMPLETE TURNOVER AND THE STRUCTURE REPRESENTS THE REOXIDISED ENZYME
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.821 α = 90 b = 60.968 β = 112.24 c = 100.326 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 1.46 30 91.9 0.05 0.05 10.2 2.1 189123 15.7
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 1.46 1.52 84.6 0.199 0.199 2.5
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QKS 1.46 30 189123 91.2 0.195 0.215 RANDOM 17.8
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 30.1 p_special_tor 15 p_staggered_tor 10.5 p_planar_tor 4.3 p_singtor_nbd 0.3 p_multtor_nbd 0.211 p_xyhbond_nbd 0.139 p_chiral_restr 0.114 p_plane_restr 0.023 p_planar_d 0.017
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 30.1 p_special_tor 15 p_staggered_tor 10.5 p_planar_tor 4.3 p_singtor_nbd 0.3 p_multtor_nbd 0.211 p_xyhbond_nbd 0.139 p_chiral_restr 0.114 p_plane_restr 0.023 p_planar_d 0.017 p_bond_d 0.013 p_angle_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 8690 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 233
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling