2RHI

Crystal structure of the 3-MBT domain from human L3MBTL1 in complex with H1.5K27me2 at 1.66 angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293L3MBTL1(197-526) (15 mg/ml in 25 mM Tris-HCl, pH 8.0, 1 mM DTT) was pre-incubated with two-fold molar excess of H1.5(23-27)K27me2 peptide. Drops were prepared by mixing 1 l complex solution with 1 l reservoir solution (7% PEG3350, 0.2 M NaAc pH 5.0). Rod-like crystals usually appear overnight and are ready for data collection after two days. Crystals were flash-frozen in liquid nitrogen with the reservoir solution augmented with an additional 30% PEG 400 as cryoprotectant prior to data collectioin., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9558.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.864α = 90
b = 93.318β = 90
c = 58.64γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.0858APS24-ID-C

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
11.66201000.0650.06531.5105640156401-3-318.4
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)
1.661.721000.460.465.19.85561

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1OZ21.66205636254919449097.40.1870.201Random20.9
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
c_angle_deg1.41
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2649
Nucleic Acid Atoms
Solvent Atoms571
Heterogen Atoms13

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling