6HPX

Crystal structure of ENL (MLLT1) in complex with compound 19


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J9S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293.1525% medium molecular weight PEG smears, 0.1M citrate, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1943.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.35α = 90
b = 48.35β = 90
c = 137.415γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-07-02MSINGLE 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)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
12.345.81000.0570.0290.99615.35.6784635.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.1690.0830.9825.8

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 REPLACEMENTTHROUGHOUT5j9s2.345.61739839099.850.213720.211370.26086RANDOM38.457
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]
-1.42-1.422.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.664
r_dihedral_angle_4_deg18.291
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg8.465
r_long_range_B_other5.641
r_long_range_B_refined5.638
r_scangle_other3.292
r_mcangle_it2.665
r_mcangle_other2.663
r_scbond_it2.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.664
r_dihedral_angle_4_deg18.291
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg8.465
r_long_range_B_other5.641
r_long_range_B_refined5.638
r_scangle_other3.292
r_mcangle_it2.665
r_mcangle_other2.663
r_scbond_it2.046
r_scbond_other2.044
r_mcbond_it1.633
r_mcbond_other1.618
r_angle_refined_deg1.261
r_angle_other_deg1.112
r_chiral_restr0.059
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1178
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing