4GFJ

Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CSBPDB entry 2CSB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP730350 mM HEPES pH 7, 0.1 M KCl, 0.01 M MgCl2, and 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.7955.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.634α = 90
b = 161.634β = 90
c = 58.227γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.9129.199.50.0690.07620.66.21928335.4
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)
12.913.0496.50.5660.5193.46.32264

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2CSB2.9129.1192831829298999.550.204730.204730.201410.267RANDOM73.398
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]
-2.21-1.11-2.213.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_dihedral_angle_4_deg16.247
r_dihedral_angle_3_deg16.226
r_dihedral_angle_1_deg5.434
r_scangle_it1.584
r_scbond_it1.086
r_angle_refined_deg1.035
r_angle_other_deg0.817
r_mcangle_it0.555
r_mcbond_it0.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_dihedral_angle_4_deg16.247
r_dihedral_angle_3_deg16.226
r_dihedral_angle_1_deg5.434
r_scangle_it1.584
r_scbond_it1.086
r_angle_refined_deg1.035
r_angle_other_deg0.817
r_mcangle_it0.555
r_mcbond_it0.282
r_chiral_restr0.056
r_mcbond_other0.039
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4940
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms19

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling