6T1N

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293.1525% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.014α = 90
b = 49.014β = 90
c = 132.425γ = 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
11.9549.011000.0820.0920.0330.9979.87.11251233.6
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)
11.952.021000.7350.840.3040.832.27.4

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 REPLACEMENTTHROUGHOUT6HQ01.9545.971187059599.860.21160.20880.266RANDOM42.801
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]
-2.27-2.274.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.717
r_dihedral_angle_4_deg20.315
r_dihedral_angle_3_deg14.272
r_dihedral_angle_1_deg8.024
r_angle_refined_deg1.199
r_angle_other_deg1.102
r_chiral_restr0.064
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.717
r_dihedral_angle_4_deg20.315
r_dihedral_angle_3_deg14.272
r_dihedral_angle_1_deg8.024
r_angle_refined_deg1.199
r_angle_other_deg1.102
r_chiral_restr0.064
r_bond_refined_d0.011
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 Atoms71
Heterogen Atoms54

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing