8SV4 | pdb_00008sv4

7-Deazapurines and 5-Halogenpyrimidine DNA duplex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EY1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62910.2 M Ammonium Sulfate, 0.1 M Sodium acetate trihydrate and 25% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
4.0969.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.539α = 90
b = 92.539β = 90
c = 78.896γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
12.327.698.90.1660.0444.213.817002
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3890.81.4711.5570.4850.5957.1

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 REPLACEMENTTHROUGHOUT2.327.61608487098.630.215990.21390.220.253550.26RANDOM50.228
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]
1.270.631.27-4.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.291
r_dihedral_angle_3_deg19.294
r_dihedral_angle_4_deg11.643
r_long_range_B_other9.494
r_long_range_B_refined9.492
r_dihedral_angle_1_deg7.975
r_scangle_other7.616
r_scbond_it5.159
r_scbond_other5.159
r_mcangle_it4.851
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.291
r_dihedral_angle_3_deg19.294
r_dihedral_angle_4_deg11.643
r_long_range_B_other9.494
r_long_range_B_refined9.492
r_dihedral_angle_1_deg7.975
r_scangle_other7.616
r_scbond_it5.159
r_scbond_other5.159
r_mcangle_it4.851
r_mcangle_other4.849
r_mcbond_it3.32
r_mcbond_other3.3
r_angle_refined_deg1.567
r_angle_other_deg0.829
r_chiral_restr0.402
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms494
Solvent Atoms79
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing