8ORO

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER HYPEROXYC 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
2.4349.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.11α = 90
b = 120.11β = 90
c = 44.82γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97932ESRFID29

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
1260.05990.1580.0935.84.54323322.1
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)
122.0598.10.7110.4061.84.7

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-VALUE260.0543216215498.8680.2290.22740.268728.482
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]
3.4263.426-6.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.618
r_dihedral_angle_4_deg20.256
r_dihedral_angle_3_deg15.281
r_dihedral_angle_1_deg6.543
r_lrange_it3.072
r_lrange_other2.806
r_angle_refined_deg1.281
r_angle_other_deg1.168
r_mcangle_it0.611
r_mcangle_other0.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.618
r_dihedral_angle_4_deg20.256
r_dihedral_angle_3_deg15.281
r_dihedral_angle_1_deg6.543
r_lrange_it3.072
r_lrange_other2.806
r_angle_refined_deg1.281
r_angle_other_deg1.168
r_mcangle_it0.611
r_mcangle_other0.611
r_scangle_it0.595
r_scangle_other0.595
r_scbond_it0.401
r_scbond_other0.401
r_mcbond_it0.391
r_mcbond_other0.391
r_nbd_other0.303
r_symmetry_nbd_refined0.29
r_symmetry_xyhbond_nbd_refined0.252
r_xyhbond_nbd_refined0.206
r_nbd_refined0.184
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_other0.167
r_nbtor_refined0.161
r_symmetry_nbtor_other0.074
r_chiral_restr0.06
r_ncsr_local_group_10.058
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4452
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing