5M9O

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1510 % PEG 1000, 10% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2745.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.243α = 90
b = 80.626β = 90.38
c = 39.289γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.4528.14960.03716.23.838367
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)
11.451.4869.90.2922.82.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OMC1.4528.1436421192095.830.230390.228920.2612RANDOM21.625
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]
0.53-0.42-0.05-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg18.25
r_dihedral_angle_3_deg12.276
r_dihedral_angle_1_deg8.439
r_long_range_B_refined4.759
r_long_range_B_other4.596
r_scangle_other2.628
r_mcangle_it2.196
r_mcangle_other2.195
r_scbond_it1.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg18.25
r_dihedral_angle_3_deg12.276
r_dihedral_angle_1_deg8.439
r_long_range_B_refined4.759
r_long_range_B_other4.596
r_scangle_other2.628
r_mcangle_it2.196
r_mcangle_other2.195
r_scbond_it1.634
r_scbond_other1.633
r_angle_refined_deg1.539
r_mcbond_other1.365
r_mcbond_it1.364
r_angle_other_deg0.959
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms1752
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing