3E1S

Structure of an N-terminal truncation of Deinococcus radiodurans RecD2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529813-18% ethanol, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.6253.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.63α = 90
b = 89.63β = 90
c = 131.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.07225ESRFID23-1

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
12.250980.03815.22.43361632947
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)
12.22.3980.3213.22.254035

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT2.220.73294630278266898.190.235410.235410.23080.28744RANDOM43.288
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]
3.38-4.090.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.963
r_dihedral_angle_3_deg18.942
r_dihedral_angle_4_deg16.719
r_dihedral_angle_1_deg5.759
r_scangle_it1.515
r_angle_refined_deg1.246
r_scbond_it1.004
r_angle_other_deg0.889
r_mcangle_it0.607
r_mcbond_it0.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.963
r_dihedral_angle_3_deg18.942
r_dihedral_angle_4_deg16.719
r_dihedral_angle_1_deg5.759
r_scangle_it1.515
r_angle_refined_deg1.246
r_scbond_it1.004
r_angle_other_deg0.889
r_mcangle_it0.607
r_mcbond_it0.499
r_symmetry_vdw_other0.263
r_xyhbond_nbd_refined0.205
r_nbd_refined0.201
r_nbd_other0.2
r_nbtor_refined0.169
r_symmetry_vdw_refined0.146
r_symmetry_hbond_refined0.095
r_mcbond_other0.092
r_nbtor_other0.088
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3889
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing