8A97

ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) UNDER XENON PRESSURE (30 bar)


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
2VAPOR DIFFUSION7293PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4248.22
48.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.86α = 90
b = 169.46β = 90
c = 169.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
12x-ray293PIXELDECTRIS PILATUS 6M2012-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96860DiamondI24

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
12.89753.58399.20.1980.0615.44.42942159.9
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)
12.8972.9595.81.120.6231.3

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 REPLACEMENTTHROUGHOUT2WJ32.89753.58329381148398.8060.1930.19180.220362.756
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]
3.4820.271-3.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.004
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg14.172
r_lrange_it7.364
r_lrange_other7.364
r_dihedral_angle_1_deg5.964
r_mcangle_it4.336
r_mcangle_other4.336
r_scangle_it3.91
r_scangle_other3.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.004
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg14.172
r_lrange_it7.364
r_lrange_other7.364
r_dihedral_angle_1_deg5.964
r_mcangle_it4.336
r_mcangle_other4.336
r_scangle_it3.91
r_scangle_other3.91
r_mcbond_it2.672
r_mcbond_other2.672
r_scbond_it2.375
r_scbond_other2.375
r_angle_other_deg1.448
r_angle_refined_deg1.312
r_nbd_other0.269
r_symmetry_nbd_refined0.208
r_nbd_refined0.202
r_symmetry_nbd_other0.176
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.127
r_chiral_restr0.081
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_refined0.059
r_ncsr_local_group_40.039
r_ncsr_local_group_10.035
r_ncsr_local_group_60.032
r_ncsr_local_group_50.029
r_ncsr_local_group_20.027
r_ncsr_local_group_30.022
r_ext_dist_refined_d0.01
r_bond_refined_d0.008
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 Atoms8966
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing