1R3G

1.16A X-ray structure of the synthetic DNA fragment with the incorporated 2'-O-[(2-Guanidinium)ethyl]-5-methyluridine residues


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
1.8834.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.111α = 90
b = 43.151β = 90
c = 45.558γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS1999-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B

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
11.1619.597.40.06517426

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.16201653589197.40.1340.1320.174RANDOM16.67
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]
0.290.15-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free11.381
r_sphericity_bonded7.752
r_scangle_it3.93
r_scbond_it3.047
r_rigid_bond_restr2.209
r_angle_refined_deg1.982
r_angle_other_deg1.267
r_xyhbond_nbd_refined0.347
r_symmetry_hbond_refined0.298
r_symmetry_vdw_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free11.381
r_sphericity_bonded7.752
r_scangle_it3.93
r_scbond_it3.047
r_rigid_bond_restr2.209
r_angle_refined_deg1.982
r_angle_other_deg1.267
r_xyhbond_nbd_refined0.347
r_symmetry_hbond_refined0.298
r_symmetry_vdw_refined0.248
r_nbd_other0.239
r_symmetry_vdw_other0.182
r_nbd_refined0.179
r_chiral_restr0.107
r_nbtor_other0.074
r_gen_planes_refined0.031
r_bond_refined_d0.02
r_bond_other_d0.009
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms418
Solvent Atoms156
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing