3O1M

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
2.4850.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.44α = 90
b = 75.95β = 107.76
c = 51.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDMAR CCD 130 mm2008-10-30MSINGLE 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
11.555099.60.04119.23.547998478062.12.1
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)
11.51.5599.60.3682.13.44763

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3BIE1.75206628902283241531980.16730.167250.165990.19073RANDOM9.917
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]
-0.43-0.11-0.380.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.786
r_dihedral_angle_4_deg13.048
r_dihedral_angle_3_deg10.796
r_dihedral_angle_1_deg5.578
r_scangle_it2.142
r_scbond_it1.342
r_angle_refined_deg1.18
r_mcangle_it0.93
r_mcbond_it0.499
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.786
r_dihedral_angle_4_deg13.048
r_dihedral_angle_3_deg10.796
r_dihedral_angle_1_deg5.578
r_scangle_it2.142
r_scbond_it1.342
r_angle_refined_deg1.18
r_mcangle_it0.93
r_mcbond_it0.499
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1571
Nucleic Acid Atoms501
Solvent Atoms329
Heterogen Atoms11

Software

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