1PVG

Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch under oil6.5293PEG 1500, Potassium Chloride, Glycerol, Sodium Cacodylate, pH 6.5, microbatch under oil, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.456α = 90
b = 71.081β = 90
c = 216.132γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-05-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.127, 0.9796ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.83089.50.0610.061226.7760367570627.502
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8672.70.430.432.84.96077

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)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 DIFFRACTIONMADTHROUGHOUT1.829.750.437603669319638589.650.208660.208660.205660.24147RANDOM23.666
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]
1.93-1.4-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.832
r_scangle_it2.574
r_scbond_it1.733
r_angle_refined_deg0.966
r_mcangle_it0.861
r_mcbond_it0.447
r_symmetry_vdw_refined0.199
r_nbd_refined0.192
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.832
r_scangle_it2.574
r_scbond_it1.733
r_angle_refined_deg0.966
r_mcangle_it0.861
r_mcbond_it0.447
r_symmetry_vdw_refined0.199
r_nbd_refined0.192
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.107
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other
r_nbtor_other
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_xyhbond_nbd_other
r_bond_other_d
r_dihedral_angle_2_deg
r_angle_other_deg
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6083
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing