2GB7

Metal-depleted Ecl18kI in complex with uncleaved, modified DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.12940.4M (NH4)H2PO4, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.697α = 90
b = 96.739β = 90
c = 192.012γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHDouble focusing X-ray optics2002-11-06MMAD
21x-ray100CCDMARRESEARCH2005-09-18MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05, 0.900, 0.9198, 0.9200MPG/DESY, HAMBURGBW6
2SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW60.9792, 0.9795MPG/DESY, HAMBURGBW6

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
1,21.74097.70.0430.043313.315849015849031
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)
1,21.71.7292.60.340.343.935907

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 DIFFRACTIONMADTHROUGHOUT1.720157798157798789897.50.2080.2080.2070.236RANDOM20.1
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]
0.410.98-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.589
r_dihedral_angle_4_deg17.786
r_dihedral_angle_3_deg15.312
r_dihedral_angle_1_deg5.09
r_scangle_it3.4
r_scbond_it2.591
r_angle_refined_deg1.475
r_mcangle_it1.463
r_mcbond_it1.18
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.589
r_dihedral_angle_4_deg17.786
r_dihedral_angle_3_deg15.312
r_dihedral_angle_1_deg5.09
r_scangle_it3.4
r_scbond_it2.591
r_angle_refined_deg1.475
r_mcangle_it1.463
r_mcbond_it1.18
r_nbtor_refined0.311
r_symmetry_vdw_refined0.288
r_symmetry_hbond_refined0.241
r_nbd_refined0.222
r_xyhbond_nbd_refined0.152
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms9695
Nucleic Acid Atoms726
Solvent Atoms602
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
GETAXphasing
DMphasing