4I9V | pdb_00004i9v

The atomic structure of 5-Hydroxymethyl 2'-deoxycitidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 436DPDB ENTRY 436D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729110% MPD,40mM cacodylate, 80mM NaCl,12 mM spermine tetrachloride, 20mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 25.606α = 90
b = 41.344β = 90
c = 64.319γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2012-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
11.0214.9980.04344.678.8366933597422
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)
11.021.0399.90.786.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUTPDB ENTRY 436D1.0214.883381632113170095.040.160640.159470.170.181890.19RANDOM22.675
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]
0.24-1.491.26
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded10.669
r_sphericity_free8.84
r_rigid_bond_restr4.594
r_angle_other_deg2.562
r_angle_refined_deg2.488
r_chiral_restr0.406
r_gen_planes_refined0.041
r_bond_refined_d0.02
r_gen_planes_other0.008
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded10.669
r_sphericity_free8.84
r_rigid_bond_restr4.594
r_angle_other_deg2.562
r_angle_refined_deg2.488
r_chiral_restr0.406
r_gen_planes_refined0.041
r_bond_refined_d0.02
r_gen_planes_other0.008
r_bond_other_d0.006
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_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms490
Solvent Atoms187
Heterogen Atoms26

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling