4EMV

Crystal structure of a topoisomerase ATP inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1inhibitor soak729318-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, inhibitor soak, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.297α = 90
b = 94.92β = 90
c = 61.247γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmonochromator2011-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID1.000APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.731.4599.80.10312.27.12383923839
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)
11.71.791000.3440.3442.17.13446

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.731.4523811121799.670.19110.18940.2233RANDOM20.758
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]
-0.02-0.220.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.362
r_dihedral_angle_4_deg13.298
r_dihedral_angle_3_deg10.619
r_dihedral_angle_1_deg4.838
r_angle_refined_deg1.024
r_angle_other_deg0.775
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.362
r_dihedral_angle_4_deg13.298
r_dihedral_angle_3_deg10.619
r_dihedral_angle_1_deg4.838
r_angle_refined_deg1.024
r_angle_other_deg0.775
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1506
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms32

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction