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Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand
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 6.7 298 45-60mM Mg Formate mixed with 12-13 mg/ml protein containing 1-5 wt% of NH4OH, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.48 α = 90 b = 140.72 β = 90 c = 229.52 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 Bent conical Si-mirror (Rh coated)
Bent Ge(111) monochromator 2009-03-07 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 1.987 57.38 100 0.094 0.094 9.8 5.7 172258 172258 14.2
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 1.99 2.03 91.5 0.303 0.303 2.5 5.5 54827
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 4BLC 1.99 57.38 171515 171515 8405 92.4 0.161 0.161 0.161 0.159 0.198 0.1582 RANDOM 18.7
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] 2.64 -3.91 1.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.61 c_scbond_it 1.89 c_mcangle_it 1.61 c_angle_deg 1.3 c_mcbond_it 1.11 c_improper_angle_d 0.92 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16068 Nucleic Acid Atoms Solvent Atoms 2266 Heterogen Atoms 176
Software Software Software Name Purpose HKL-3000 data collection CNS refinement MOSFLM data reduction SCALA data scaling CNS phasing