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Crystal Structure of Manganese Catalase from Lactobacillus plantarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other hexamer of Thermus thermophilus Mn catalase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PEG 8000, TAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.72 α = 90 b = 96.42 β = 106.88 c = 106.69 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 298 IMAGE PLATE MARRESEARCH 1996-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8900 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.84 17 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.839 1.886 63.6 0.136 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT hexamer of Thermus thermophilus Mn catalase 1.84 14.94 1 2 125298 107466 5735 90.3 0.1469 0.14691 0.14479 0.18694 RANDOM 19.072
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] -0.03 -0.4 -0.14 -0.07
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 5.382 p_scbond_it 3.281 p_mcangle_it 1.739 p_angle_d 1.671 p_mcbond_it 0.938 p_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12504 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 36
Software Software Software Name Purpose DM model building REFMAC refinement DENZO data reduction SCALEPACK data scaling DM phasing