4A75

The Lin28b Cold shock domain in complex with hexathymidine.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2770.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 M sodium thiocyanate as reservoir buffer
Crystal Properties
Matthews coefficientSolvent content
2.2645.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.799α = 90
b = 81.822β = 90
c = 99.819γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSYBESSYBL14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.7532.9189.40.060.07813.22.5391882
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.8587.80.393.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONOTHERTHROUGHOUTNONE1.7532.914008821101000.172390.171050.19801RANDOM14.67
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]
-0.280.67-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.172
r_dihedral_angle_4_deg17.295
r_dihedral_angle_3_deg11.963
r_dihedral_angle_1_deg6.292
r_scangle_it4.778
r_scbond_it3.59
r_mcangle_it2.71
r_mcbond_it1.731
r_angle_refined_deg1.476
r_angle_other_deg0.983
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.172
r_dihedral_angle_4_deg17.295
r_dihedral_angle_3_deg11.963
r_dihedral_angle_1_deg6.292
r_scangle_it4.778
r_scbond_it3.59
r_mcangle_it2.71
r_mcbond_it1.731
r_angle_refined_deg1.476
r_angle_other_deg0.983
r_mcbond_other0.476
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2734
Nucleic Acid Atoms400
Solvent Atoms506
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement