5ZZ1

Probing the active center of catalase-phenol oxidase from Scytalidium thermophilum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AUM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2PROTEIN CRYSTAL WAS OBTAINED IN 6-16 % PEG400, 0.2 M POTASSIUM CHLORIDE, 0.01 M CALCIUM CHLORIDE DEHYDRATE AND 0.05 M SODIUM CACODYLATE TRIHYDRATE AT PH 5.2
Crystal Properties
Matthews coefficientSolvent content
2.3246.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.528α = 90
b = 121.677β = 102.16
c = 185.454γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.0DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9129.499.80.0570.0370.99810.23.3206818
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.9694.60.4260.2350.8432.73.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4AUM1.9129.41964371038198.770.14370.14210.1737RANDOM20.604
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]
-0.110.50.01-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.865
r_dihedral_angle_4_deg18.019
r_dihedral_angle_3_deg13.019
r_dihedral_angle_1_deg7.024
r_angle_refined_deg1.937
r_angle_other_deg1.064
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.865
r_dihedral_angle_4_deg18.019
r_dihedral_angle_3_deg13.019
r_dihedral_angle_1_deg7.024
r_angle_refined_deg1.937
r_angle_other_deg1.064
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21107
Nucleic Acid Atoms
Solvent Atoms1646
Heterogen Atoms241

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction