4RO7

Sequence and structure of a self-assembled 3-D DNA crystal: D(GGAAAGCTTGGAG)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P1YPDB ENTRY 1P1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION298120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1661.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.317α = 90
b = 40.317β = 90
c = 54.958γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979200APS24-ID-C

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
12.0354.960.0326.353297
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)
12.032.142.1710.95.1482

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1P1Y2.0334.92295227797.320.224550.221860.25134RANDOM82.706
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]
0.330.160.33-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.073
r_long_range_B_other4.938
r_scangle_other3.86
r_scbond_other2.385
r_scbond_it2.383
r_angle_other_deg1.699
r_angle_refined_deg1.173
r_chiral_restr0.074
r_gen_planes_refined0.01
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.073
r_long_range_B_other4.938
r_scangle_other3.86
r_scbond_other2.385
r_scbond_it2.383
r_angle_other_deg1.699
r_angle_refined_deg1.173
r_chiral_restr0.074
r_gen_planes_refined0.01
r_bond_refined_d0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms254
Solvent Atoms7
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement