3G4T

Mth0212 (WT) in complex with a 7bp dsDNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293reservoir: 40mM MgAc/50mM sodium cacodylate pH 6.0/30% (v/v) MPD; complex solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.9257.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.764α = 90
b = 79.6β = 90
c = 99.409γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.21.00605BESSY14.2

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
12.645097.90.04736.27.623676
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.642.7383.10.4172.54.6

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 3FZI2.6442.5722367121397.420.243190.240460.29684RANDOM67.685
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]
2.78-4.291.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_3_deg18.241
r_dihedral_angle_4_deg17.209
r_dihedral_angle_1_deg6.832
r_scangle_it1.952
r_angle_refined_deg1.335
r_mcangle_it1.246
r_scbond_it1.176
r_mcbond_it0.708
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_3_deg18.241
r_dihedral_angle_4_deg17.209
r_dihedral_angle_1_deg6.832
r_scangle_it1.952
r_angle_refined_deg1.335
r_mcangle_it1.246
r_scbond_it1.176
r_mcbond_it0.708
r_nbtor_refined0.314
r_symmetry_vdw_refined0.298
r_symmetry_hbond_refined0.227
r_nbd_refined0.211
r_xyhbond_nbd_refined0.177
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4248
Nucleic Acid Atoms278
Solvent Atoms16
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling