5JQR

The Structure of Ascorbate Peroxidase Compound II formed by reaction with m-CPBA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XIF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3002.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.095α = 90
b = 82.095β = 90
c = 75.162γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2015-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.815898.610.169.46.822667
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)
11.811.840.69

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 REPLACEMENTFREE R-VALUE2XIF1.815822667119098.610.156510.153550.21421RANDOM15.615
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]
0.10.1-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.277
r_dihedral_angle_4_deg22.656
r_dihedral_angle_3_deg13.858
r_long_range_B_refined6.954
r_long_range_B_other6.119
r_dihedral_angle_1_deg5.984
r_scangle_other3.199
r_scbond_it2.167
r_mcangle_it2.1
r_mcangle_other2.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.277
r_dihedral_angle_4_deg22.656
r_dihedral_angle_3_deg13.858
r_long_range_B_refined6.954
r_long_range_B_other6.119
r_dihedral_angle_1_deg5.984
r_scangle_other3.199
r_scbond_it2.167
r_mcangle_it2.1
r_mcangle_other2.099
r_scbond_other2.073
r_angle_refined_deg1.979
r_mcbond_it1.468
r_mcbond_other1.45
r_angle_other_deg1.131
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_other0.014
r_gen_planes_refined0.013
r_bond_other_d0.003
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 Atoms1905
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing