6HPW

Crystal structure of ENL (MLLT1) in complex with compound 20


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 acetate, 0.1M bis-tris, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.1342.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.738α = 90
b = 48.738β = 90
c = 131.623γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-24MSINGLE 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
11.948.741000.1150.0340.99910.812.81329230.4
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)
11.91.941000.8550.2570.95312.8

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 REPLACEMENTTHROUGHOUT5j9s1.945.711258064199.920.216570.213390.28102RANDOM42.073
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]
-1.51-1.513.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.294
r_dihedral_angle_4_deg19.981
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg8.065
r_long_range_B_refined7.21
r_long_range_B_other7.209
r_scangle_other3.609
r_scbond_it2.527
r_scbond_other2.526
r_mcangle_it2.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.294
r_dihedral_angle_4_deg19.981
r_dihedral_angle_3_deg12.677
r_dihedral_angle_1_deg8.065
r_long_range_B_refined7.21
r_long_range_B_other7.209
r_scangle_other3.609
r_scbond_it2.527
r_scbond_other2.526
r_mcangle_it2.382
r_mcangle_other2.38
r_mcbond_it1.555
r_mcbond_other1.552
r_angle_refined_deg1.538
r_angle_other_deg1.242
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_gen_planes_other0.004
r_bond_other_d0.002
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 Atoms1174
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing