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Cytochrome cd1 Nitrite Reductase, CO 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 PHOSPHATE BUFFER PH 7 AND 15 % GLYCEROL. CO WAS INTRODUCED UNDER 15 ATM PRESSURE FOR 20 MINUTES AT -20 DEGREES.
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.94 α = 90 b = 61.04 β = 111.77 c = 100.39 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 1.57 30 87.3 0.04 0.04 12 2.1 148443 15.718
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 1.57 1.64 83.7 0.17 0.17 2.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AOF 1.6 30 140697 88.7 0.178 0.1778 0.199 0.1973 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 31.2 p_special_tor 15 p_staggered_tor 12.3 p_planar_tor 7.3 p_multtor_nbd 0.238 p_singtor_nbd 0.175 p_xyhbond_nbd 0.143 p_chiral_restr 0.101 p_planar_d 0.05 p_angle_d 0.024
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 31.2 p_special_tor 15 p_staggered_tor 12.3 p_planar_tor 7.3 p_multtor_nbd 0.238 p_singtor_nbd 0.175 p_xyhbond_nbd 0.143 p_chiral_restr 0.101 p_planar_d 0.05 p_angle_d 0.024 p_plane_restr 0.023 p_bond_d 0.01 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 7567 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling