5JPR

Neutron Structure of Compound II of Ascorbate Peroxidase


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP83002.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9
Crystal Properties
Matthews coefficientSolvent content
2.2344.91

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
11neutron100IMAGE PLATEMAATEL IMAGINEmultilayer2015-10-14LLAUE
21x-ray100CCDRIGAKU SATURN 944+multilayer2015-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1NUCLEAR REACTORILL BEAMLINE LADI III3.2 - 4.2ILLLADI III
2ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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)R Split (All)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
12.24069.80.18749220
21.819.9198.720.169.46.823857

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.80619.911.3623857119498.720.15780.15470.2159
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.20236.7142.03922046268.140.24010.23640.3104
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]
0.48890.4889-0.9778
0.48890.4889-0.9778
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.898
f_dihedral_angle_d11.898
f_angle_d1.366
f_angle_d1.366
f_chiral_restr0.115
f_chiral_restr0.115
f_bond_d0.016
f_bond_d0.016
f_plane_restr0.009
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1899
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms54

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing