6HPY

Crystal structure of ENL (MLLT1) in complex with compound 12


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% PEG 3350, 0.2M ammonium sulfate, 0.1M bis-tris, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.039α = 90
b = 49.039β = 90
c = 132.729γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
1266.391000.0790.030.99615.78.61169129.3
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)
122.051000.2160.080.9877.78.9

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 REPLACEMENTTHROUGHOUT5j9s2461096757799.240.2190.216890.26031RANDOM36.577
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]
-2.57-2.575.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.038
r_dihedral_angle_4_deg25.472
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg7.125
r_long_range_B_refined7.05
r_long_range_B_other7.048
r_scangle_other3.199
r_mcangle_it2.431
r_mcangle_other2.43
r_scbond_it1.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.038
r_dihedral_angle_4_deg25.472
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg7.125
r_long_range_B_refined7.05
r_long_range_B_other7.048
r_scangle_other3.199
r_mcangle_it2.431
r_mcangle_other2.43
r_scbond_it1.993
r_scbond_other1.991
r_mcbond_it1.523
r_mcbond_other1.514
r_angle_refined_deg1.434
r_angle_other_deg1.177
r_chiral_restr0.072
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
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 Atoms1169
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing