6T1O

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HQ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1525% PEG 3350, 0.2M sodium chloride, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1743.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.027α = 90
b = 49.027β = 90
c = 131.431γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.949.0397.50.0770.090.0380.9918.74.81300831
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9794.80.4180.4590.2170.9132.64.5

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 REPLACEMENTTHROUGHOUT6HQ01.945.941229765796.980.20480.20220.2507RANDOM39.136
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]
-3.29-3.296.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.59
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg15.545
r_dihedral_angle_1_deg8.056
r_angle_refined_deg1.287
r_angle_other_deg1.167
r_chiral_restr0.07
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.59
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg15.545
r_dihedral_angle_1_deg8.056
r_angle_refined_deg1.287
r_angle_other_deg1.167
r_chiral_restr0.07
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms71

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing