3O1P

Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BIEPDB entry 3BIE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% (w/v) PEG 8K, 100 mM Sodium Chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5,, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4950.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.4α = 90
b = 75.93β = 107.94
c = 51.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9266APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5150970.34114.43.443144418502.92.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.58950.3412.22.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3BIE1.51202.22.23918338952204799.410.182050.180360.21493RANDOM16.89
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]
0.13-0.090.05-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36
r_dihedral_angle_4_deg14.437
r_dihedral_angle_3_deg11.69
r_dihedral_angle_1_deg5.79
r_scangle_it1.823
r_angle_refined_deg1.212
r_scbond_it1.175
r_mcangle_it0.822
r_mcbond_it0.431
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36
r_dihedral_angle_4_deg14.437
r_dihedral_angle_3_deg11.69
r_dihedral_angle_1_deg5.79
r_scangle_it1.823
r_angle_refined_deg1.212
r_scbond_it1.175
r_mcangle_it0.822
r_mcbond_it0.431
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1580
Nucleic Acid Atoms504
Solvent Atoms347
Heterogen Atoms17

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling