2EWF

Crystal structure of the site-specific DNA nickase N.BspD6I


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22980.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (v/v) glycerol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7254.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.553α = 90
b = 92.562β = 111.88
c = 76.349γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-07-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW60.9198, 0.9200, 1.05MPG/DESY, HAMBURGBW6

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
11.842099.90.0812.66752322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.87100

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADFREE R1.84106611762804333099.80.20030.20.18290.236RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
75358.79
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.12
s_similar_adp_cmpnt0.087
s_non_zero_chiral_vol0.04
s_zero_chiral_vol0.034
s_from_restr_planes0.024
s_angle_d0.022
s_anti_bump_dis_restr0.008
s_bond_d0.007
s_similar_dist
s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4861
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms13

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing