7OJM

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 NORMOXIC CONDITIONS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CFS 

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 = 119.19α = 90
b = 119.19β = 90
c = 44.44γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91741DiamondI04-1

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
1244.4499.30.1080.0510.56.44236027.6
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)
122.050.7370.4071.8

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-VALUE4CFS2.00142.1442343211699.2430.2060.20410.236732.536
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]
8.0488.048-16.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg19.131
r_dihedral_angle_3_deg15.157
r_dihedral_angle_1_deg6.766
r_lrange_it5.225
r_lrange_other5.128
r_scangle_it3.131
r_scangle_other3.131
r_mcangle_it3.12
r_mcangle_other3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.832
r_dihedral_angle_4_deg19.131
r_dihedral_angle_3_deg15.157
r_dihedral_angle_1_deg6.766
r_lrange_it5.225
r_lrange_other5.128
r_scangle_it3.131
r_scangle_other3.131
r_mcangle_it3.12
r_mcangle_other3.12
r_mcbond_it2.133
r_mcbond_other2.133
r_scbond_it2.097
r_scbond_other2.097
r_angle_refined_deg1.335
r_angle_other_deg1.183
r_nbd_other0.296
r_symmetry_nbd_refined0.244
r_metal_ion_refined0.242
r_xyhbond_nbd_refined0.217
r_nbd_refined0.206
r_symmetry_nbd_other0.193
r_symmetry_xyhbond_nbd_refined0.17
r_nbtor_refined0.161
r_symmetry_xyhbond_nbd_other0.126
r_symmetry_nbtor_other0.078
r_chiral_restr0.064
r_ncsr_local_group_10.028
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4444
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing