4HIG

Ultrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162921.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR MN2+ SOAKING, A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK.
Crystal Properties
Matthews coefficientSolvent content
1.5922.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 17.732α = 90
b = 31.436β = 90
c = 43.935γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-12-04MSINGLE WAVELENGTH
21x-ray100CCDRAYONIX MX-2252012-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12
2SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
10.7525.5779.90.05319.283.2847730-34.756
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)
10.750.7710.60.03811.391.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R1I0T0.7525.5747730100979.90.0710.0710.081RANDOM
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
1164332.97
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.069
s_similar_adp_cmpnt0.037
s_angle_d0.029
s_anti_bump_dis_restr0.028
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms240
Solvent Atoms92
Heterogen Atoms15

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling