3IGC

Smallpox virus topoisomerase-DNA transition state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4294pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties
Matthews coefficientSolvent content
2.7154.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.999α = 90
b = 103.999β = 90
c = 93.01γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315r2007-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
125096.30.07221.58.9276922
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)
22.1598.50.5233.38.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2H7G EXCLUDING DNA DOWNSTREAM OF CLEAVAGE SITE AND AMINO ACID RESIDUES 240-3142.150276921490960.180.1770.244RANDOM44.78
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]
0.030.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg20.232
r_dihedral_angle_3_deg17.874
r_dihedral_angle_1_deg5.754
r_scangle_it2.917
r_scbond_it2.103
r_angle_refined_deg1.74
r_mcangle_it1.261
r_mcbond_it0.715
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg20.232
r_dihedral_angle_3_deg17.874
r_dihedral_angle_1_deg5.754
r_scangle_it2.917
r_scbond_it2.103
r_angle_refined_deg1.74
r_mcangle_it1.261
r_mcbond_it0.715
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms2587
Nucleic Acid Atoms647
Solvent Atoms426
Heterogen Atoms3

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling