6PM7

The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Vapor diffusion with 10 ul drops and 0.6 ml reservoirs. Reservoirs were 6% PEG 3350 buffered with 0.1 M MES at pH 6.5. Drops were equal amounts of 35 mg/ml protein in H2O and reservoir solution. Growth time about two weeks.
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.865α = 90
b = 140.865β = 90
c = 101.84γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS 300K2018-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8512298.70.1420.140.1450.0330.9989.817.497987
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8889.42.592.592.911.010.5010.37.9

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 REPLACEMENTTHROUGHOUT1.85121.9992909494098.540.193630.191520.23248RANDOM52.633
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]
-0.91-0.46-0.912.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.009
r_dihedral_angle_4_deg19.86
r_dihedral_angle_3_deg14.571
r_long_range_B_refined8.173
r_long_range_B_other8.164
r_dihedral_angle_1_deg7.296
r_scangle_other6.651
r_scbond_it5.184
r_scbond_other5.178
r_mcangle_it4.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.009
r_dihedral_angle_4_deg19.86
r_dihedral_angle_3_deg14.571
r_long_range_B_refined8.173
r_long_range_B_other8.164
r_dihedral_angle_1_deg7.296
r_scangle_other6.651
r_scbond_it5.184
r_scbond_other5.178
r_mcangle_it4.715
r_mcangle_other4.715
r_mcbond_it3.895
r_mcbond_other3.893
r_angle_refined_deg1.391
r_angle_other_deg1.259
r_chiral_restr0.067
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.002
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8016
Nucleic Acid Atoms
Solvent Atoms708
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing