7SJG

Structure of Dehaloperoxidase B in Complex with Thymoquinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277MPEG 2000, ammonium sulfate, Na cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.1743.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.358α = 90
b = 67.565β = 90
c = 67.825γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2021-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

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
11.444.299.90.99917.14.753478
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)
11.41.4360.541

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IXF1.444.253478268699.9230.1450.14240.194921.02
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]
2.294-3.3791.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.051
r_dihedral_angle_4_deg22.573
r_dihedral_angle_3_deg17.134
r_scangle_other10.011
r_scangle_it9.995
r_lrange_it8.968
r_lrange_other8.922
r_scbond_other8.901
r_scbond_it8.884
r_dihedral_angle_1_deg6.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.051
r_dihedral_angle_4_deg22.573
r_dihedral_angle_3_deg17.134
r_scangle_other10.011
r_scangle_it9.995
r_lrange_it8.968
r_lrange_other8.922
r_scbond_other8.901
r_scbond_it8.884
r_dihedral_angle_1_deg6.005
r_rigid_bond_restr5.314
r_mcangle_other4.505
r_mcangle_it4.501
r_mcbond_it3.714
r_mcbond_other3.713
r_angle_refined_deg2.258
r_angle_other_deg1.704
r_dihedral_angle_other_3_deg1.17
r_symmetry_nbd_refined0.306
r_nbd_other0.296
r_nbd_refined0.295
r_symmetry_xyhbond_nbd_other0.27
r_symmetry_nbd_other0.23
r_xyhbond_nbd_refined0.211
r_symmetry_xyhbond_nbd_refined0.196
r_nbtor_refined0.194
r_chiral_restr0.119
r_symmetry_nbtor_other0.091
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2133
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing