2V8U

Atomic resolution structure of Mn catalase from Thermus Thermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19.5pH 9.5
Crystal Properties
Matthews coefficientSolvent content
2.9959

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.3α = 90
b = 132.3β = 90
c = 132.3γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1996-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.055099.90.07174345906
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)
11.051.0799.50.2734

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.0595.35353747105899.80.1060.1060.121RANDOM9.57
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.974
r_scangle_it3.842
r_scbond_it2.639
r_mcangle_it1.979
r_angle_refined_deg1.962
r_angle_other_deg1.676
r_mcbond_it1.396
r_bond_other_d0.722
r_symmetry_vdw_other0.326
r_xyhbond_nbd_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.974
r_scangle_it3.842
r_scbond_it2.639
r_mcangle_it1.979
r_angle_refined_deg1.962
r_angle_other_deg1.676
r_mcbond_it1.396
r_bond_other_d0.722
r_symmetry_vdw_other0.326
r_xyhbond_nbd_refined0.307
r_symmetry_hbond_refined0.298
r_nbd_refined0.287
r_nbd_other0.272
r_symmetry_vdw_refined0.206
r_chiral_restr0.141
r_gen_planes_other0.099
r_nbtor_other0.089
r_gen_planes_refined0.05
r_bond_refined_d0.02
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4692
Nucleic Acid Atoms
Solvent Atoms1077
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing