2XJ6

The structure of ferrous ascorbate peroxidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OAFPDB ENTRY 1OAF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.3LISO4 2.25 M HEPES 0.1 M PH 8.3
Crystal Properties
Matthews coefficientSolvent content
2.3648

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.24α = 90
b = 82.24β = 90
c = 75.38γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.736.7894.50.119.13.727116
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)
11.71.7996.30.562.43.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1OAF1.736.7825721139593.340.172520.169730.22545RANDOM18.795
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.593
r_dihedral_angle_4_deg26.193
r_dihedral_angle_3_deg15.695
r_scangle_it9.548
r_scbond_it6.673
r_mcangle_it5.35
r_dihedral_angle_1_deg5.004
r_mcbond_it4.028
r_angle_refined_deg2.034
r_chiral_restr0.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.593
r_dihedral_angle_4_deg26.193
r_dihedral_angle_3_deg15.695
r_scangle_it9.548
r_scbond_it6.673
r_mcangle_it5.35
r_dihedral_angle_1_deg5.004
r_mcbond_it4.028
r_angle_refined_deg2.034
r_chiral_restr0.047
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms1903
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing