3SSD

DNA binding domain of restriction endonuclease bound to DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop6.82920.2 M LiCl, 18% PEG4000, pH 6.8, sitting drop, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.7535.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.085α = 90
b = 67.189β = 90
c = 142.414γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100FLAT PANELMAR5552008-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81500EMBL/DESY, HAMBURGX11

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
12.229.0399.80.070.0718.85.618339
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)
12.22.3299.90.2540.2541.25.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUT2.219.021647416474179499.510.201990.19550.26221RANDOM42.829
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]
-2.572.83-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_dihedral_angle_4_deg24.19
r_dihedral_angle_3_deg16.067
r_dihedral_angle_1_deg6.62
r_scangle_it3.23
r_scbond_it2.473
r_mcangle_it1.826
r_angle_refined_deg1.353
r_mcbond_it1.144
r_nbtor_refined0.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_dihedral_angle_4_deg24.19
r_dihedral_angle_3_deg16.067
r_dihedral_angle_1_deg6.62
r_scangle_it3.23
r_scbond_it2.473
r_mcangle_it1.826
r_angle_refined_deg1.353
r_mcbond_it1.144
r_nbtor_refined0.287
r_nbd_refined0.143
r_symmetry_vdw_refined0.112
r_chiral_restr0.088
r_xyhbond_nbd_refined0.083
r_symmetry_hbond_refined0.069
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2483
Nucleic Acid Atoms487
Solvent Atoms136
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing