9THS | pdb_00009ths

Room temperature structure of Ascorbate Peroxidase at 1.54A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OAG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298.70.1M HEPES, 2.7M Magnesium Sulphate
Crystal Properties
Matthews coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.831α = 90
b = 82.831β = 90
c = 76.017γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298.7PIXELRIGAKU HyPix-6000HE2025-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5417

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.5429.2999.90.9978.811.342926
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.540.999

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5428.01942877211999.90.1680.16670.17320.20130.2051RANDOM16.646
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]
-0.63-0.631.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.901
r_dihedral_angle_2_deg12.706
r_dihedral_angle_3_deg12.176
r_lrange_other9.933
r_lrange_it9.911
r_scangle_it9.106
r_scangle_other9.103
r_rigid_bond_restr6.613
r_scbond_other6.4
r_scbond_it6.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.901
r_dihedral_angle_2_deg12.706
r_dihedral_angle_3_deg12.176
r_lrange_other9.933
r_lrange_it9.911
r_scangle_it9.106
r_scangle_other9.103
r_rigid_bond_restr6.613
r_scbond_other6.4
r_scbond_it6.384
r_dihedral_angle_1_deg6.004
r_mcangle_it5.274
r_mcangle_other5.272
r_mcbond_other3.554
r_mcbond_it3.553
r_angle_refined_deg1.939
r_dihedral_angle_other_2_deg1.055
r_angle_other_deg0.678
r_xyhbond_nbd_refined0.224
r_nbd_refined0.217
r_symmetry_nbd_other0.187
r_nbtor_refined0.184
r_symmetry_nbd_refined0.179
r_nbd_other0.16
r_chiral_restr0.106
r_symmetry_xyhbond_nbd_refined0.095
r_symmetry_nbtor_other0.076
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1904
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing