3UWP

Crystal structure of Dot1l in complex with 5-iodotubercidin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.62913.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.4664.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.784α = 90
b = 149.784β = 90
c = 53.521γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.91963APS23-ID-D

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
12.055099.60.0988.85.943269
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)
12.052.1296.70.9734.54142

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.054043105209299.4070.1960.19510.2231FROM PDB ENTRY 3QOW35.82
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]
-1.959-0.98-1.9592.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.233
r_dihedral_angle_4_deg17.8
r_dihedral_angle_3_deg13.411
r_dihedral_angle_1_deg5.435
r_angle_refined_deg1.327
r_angle_other_deg0.879
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.233
r_dihedral_angle_4_deg17.8
r_dihedral_angle_3_deg13.411
r_dihedral_angle_1_deg5.435
r_angle_refined_deg1.327
r_angle_other_deg0.879
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2669
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms29

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction