7OKZ

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL- QUINOLIN-4(1H)-ONE UNDER HYPEROXIC CONDITIONS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OJM 

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
2.3848.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.52α = 90
b = 120.52β = 90
c = 44.74γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
12.160.2699.40.090.04112.76.33776128.1
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)
12.12.160.7580.487

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 REPLACEMENTFREE R-VALUE7OJM2.10160.2637749179399.3580.1920.19020.228435.554
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]
0.720.72-1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg16.592
r_dihedral_angle_3_deg14.771
r_dihedral_angle_1_deg6.449
r_lrange_it5.821
r_lrange_other5.733
r_scangle_it3.865
r_scangle_other3.865
r_mcangle_it3.482
r_mcangle_other3.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg16.592
r_dihedral_angle_3_deg14.771
r_dihedral_angle_1_deg6.449
r_lrange_it5.821
r_lrange_other5.733
r_scangle_it3.865
r_scangle_other3.865
r_mcangle_it3.482
r_mcangle_other3.482
r_scbond_it2.637
r_scbond_other2.637
r_mcbond_it2.414
r_mcbond_other2.413
r_angle_refined_deg1.324
r_angle_other_deg1.212
r_nbd_other0.296
r_symmetry_nbd_refined0.266
r_metal_ion_refined0.236
r_xyhbond_nbd_refined0.216
r_nbd_refined0.198
r_symmetry_nbd_other0.191
r_symmetry_xyhbond_nbd_refined0.167
r_nbtor_refined0.16
r_symmetry_nbtor_other0.077
r_chiral_restr0.064
r_ncsr_local_group_10.053
r_symmetry_xyhbond_nbd_other0.043
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4461
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing