3GP8

Crystal structure of the binary complex of RecD2 with DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529815% PEG 8000, 2-6% Ethylene glycol, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6553.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.14α = 90
b = 90.32β = 90
c = 142.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.55098.80.0320.03233.74.92487724589-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.691.80.1750.17584.32492

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3E1S2.545.182333223332125698.990.230230.230230.228150.26827RANDOM37.8
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.779
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg17.75
r_dihedral_angle_1_deg5.212
r_angle_refined_deg1.146
r_angle_other_deg0.885
r_nbd_refined0.22
r_symmetry_hbond_refined0.208
r_nbd_other0.196
r_symmetry_vdw_other0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.779
r_dihedral_angle_4_deg17.946
r_dihedral_angle_3_deg17.75
r_dihedral_angle_1_deg5.212
r_angle_refined_deg1.146
r_angle_other_deg0.885
r_nbd_refined0.22
r_symmetry_hbond_refined0.208
r_nbd_other0.196
r_symmetry_vdw_other0.195
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.153
r_nbtor_other0.086
r_symmetry_vdw_refined0.045
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_chiral_restr
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4088
Nucleic Acid Atoms157
Solvent Atoms190
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling