1JKU

Crystal Structure of Manganese Catalase from Lactobacillus plantarum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherhexamer of Thermus thermophilus Mn catalase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291PEG 8000, TAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal Properties
Matthews coefficientSolvent content
2.0640.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.72α = 90
b = 96.42β = 106.88
c = 106.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCH1996-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8900EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8417-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.8391.88663.60.1363

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUThexamer of Thermus thermophilus Mn catalase1.8414.9412125298107466573590.30.14690.146910.144790.18694RANDOM19.072
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
KeyRefinement Restraint Deviation
p_scangle_it5.382
p_scbond_it3.281
p_mcangle_it1.739
p_angle_d1.671
p_mcbond_it0.938
p_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12504
Nucleic Acid Atoms
Solvent Atoms989
Heterogen Atoms36

Software

Software
Software NamePurpose
DMmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing