1R2O | pdb_00001r2o

d(GCATGCT) + Ni2+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7290sodium cacodylate, nickel dichloride, potassium chloride, MPD, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.8634.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.807α = 90
b = 24.807β = 90
c = 92.081γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8126EMBL/DESY, HAMBURGX11

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
12.3830.7199.50.0829.913.4785731.357
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)
2.382.5199.90.216417.1119

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3830.718012299.30.225580.22440.240.245960.26RANDOM30.848
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]
0.260.130.26-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.214
r_angle_refined_deg2.467
r_scbond_it2.173
r_angle_other_deg1.191
r_symmetry_vdw_other0.233
r_nbd_other0.2
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.136
r_nbd_refined0.121
r_symmetry_hbond_refined0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.214
r_angle_refined_deg2.467
r_scbond_it2.173
r_angle_other_deg1.191
r_symmetry_vdw_other0.233
r_nbd_other0.2
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.136
r_nbd_refined0.121
r_symmetry_hbond_refined0.103
r_nbtor_other0.091
r_chiral_restr0.072
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms160
Solvent Atoms8
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
XTALVIEWrefinement