3OMC

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O4XPDB ENTRY 2O4X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529130% PEG1500, 1:500 V8 PROTEASE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
1.7630.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.622α = 90
b = 75.834β = 90.37
c = 80.177γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCVariMax HR2010-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
11.775099.60.0418.83.641508
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)
1.771.83980.2823.54035

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2O4X1.7725.0541488208899.710.18030.17860.2131RANDOM29.3425
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]
1.22-0.85-0.43-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.118
r_dihedral_angle_3_deg12.657
r_dihedral_angle_4_deg11.324
r_dihedral_angle_1_deg5.452
r_angle_refined_deg1.175
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3501
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling