2YPB

Structure of the SCL:E47 complex bound to DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
165 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE
Crystal Properties
Matthews coefficientSolvent content
2.860

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.193α = 90
b = 152.882β = 90
c = 55.412γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
12.9397.80.0815.63.872031.2
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)
12.9398.50.971.53.7

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 2YPA2.8742.44686033196.930.255310.253810.28828RANDOM117.195
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]
8.14-3.96-4.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.275
r_dihedral_angle_3_deg14.846
r_dihedral_angle_4_deg12.082
r_scangle_it7.857
r_scbond_it5.226
r_mcangle_it5.215
r_dihedral_angle_1_deg4.145
r_mcbond_it3.057
r_angle_refined_deg0.804
r_chiral_restr0.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.275
r_dihedral_angle_3_deg14.846
r_dihedral_angle_4_deg12.082
r_scangle_it7.857
r_scbond_it5.226
r_mcangle_it5.215
r_dihedral_angle_1_deg4.145
r_mcbond_it3.057
r_angle_refined_deg0.804
r_chiral_restr0.042
r_bond_refined_d0.005
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1174
Nucleic Acid Atoms448
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing