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Structural and Kinetic Analysis of the Beef liver Catalase interacting with Nitric Oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BLC PDB entry 4BLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 45-60 mM Mg formate,12-13mg/ml protein containing 1-5 wt% of NH4OH (30% in water)
soaking these crystals overnight in an 80 mM Mg-Formate solution, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277 K
Crystal Properties Matthews coefficient Solvent content 2.92 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.22 α = 90 b = 140.92 β = 90 c = 229.37 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 QUANTUM 315 2009-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.9 38.4 100 0.089 0.089 11.8 3.6 206799 206799 18.9
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 1.9 2 97.1 0.291 0.291 2.5 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4BLC 1.9 38.4 206799 206799 10167 97.3 0.221 0.221 0.2196 0.259 0.2188 RANDOM 26.9
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] 1.55 -6.43 4.88
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.49 c_scbond_it 1.87 c_mcangle_it 1.83 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 1.03 c_bond_d 0.007 c_dihedral_angle_d_na c_dihedral_angle_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.49 c_scbond_it 1.87 c_mcangle_it 1.83 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 1.03 c_bond_d 0.007 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 16068 Nucleic Acid Atoms Solvent Atoms 1283 Heterogen Atoms 172
Software Software Software Name Purpose ADSC data collection CNS refinement MOSFLM data reduction SCALA data scaling CNS phasing