8OXT

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) H251A VARIANT COMPLEXED WITH N-ACETYLANTHRANILATE AS RESULT OF IN CRYSTALLO TURNOVER OF ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE UNDER HYPEROXIC CONDITIONS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WJ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4149.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.06α = 90
b = 120.06β = 90
c = 44.5γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97981ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (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
1229.1297.90.0740.03320.16.942489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0589.90.6390.5351.4

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.00329.1237765191087.4210.2050.2030.235526.706
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]
0.6830.683-1.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.939
r_dihedral_angle_3_deg16.855
r_dihedral_angle_4_deg16.759
r_dihedral_angle_1_deg6.961
r_lrange_it4.657
r_lrange_other4.599
r_scangle_it2.708
r_scangle_other2.708
r_mcangle_it2.703
r_mcangle_other2.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.939
r_dihedral_angle_3_deg16.855
r_dihedral_angle_4_deg16.759
r_dihedral_angle_1_deg6.961
r_lrange_it4.657
r_lrange_other4.599
r_scangle_it2.708
r_scangle_other2.708
r_mcangle_it2.703
r_mcangle_other2.701
r_mcbond_it1.863
r_mcbond_other1.862
r_scbond_it1.825
r_scbond_other1.825
r_angle_refined_deg1.387
r_angle_other_deg1.203
r_symmetry_nbd_refined0.438
r_nbd_other0.428
r_nbd_refined0.223
r_symmetry_xyhbond_nbd_refined0.212
r_symmetry_nbd_other0.191
r_xyhbond_nbd_refined0.188
r_metal_ion_refined0.175
r_nbtor_refined0.162
r_symmetry_nbtor_other0.076
r_chiral_restr0.066
r_ncsr_local_group_10.045
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4440
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing