5A3T

Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid).


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
Crystal Properties
Matthews coefficientSolvent content
2.0740.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.852α = 90
b = 141.852β = 90
c = 151.509γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2015-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.947.711000.123.422.3710272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921001.52.322.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 51AF1.9122.8567433353499.960.200460.199440.22039RANDOM39.632
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]
0.270.130.27-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.217
r_dihedral_angle_4_deg15.976
r_dihedral_angle_3_deg12.448
r_dihedral_angle_1_deg6.043
r_mcangle_it3.559
r_scbond_it2.77
r_mcbond_it2.268
r_mcbond_other2.268
r_angle_refined_deg1.497
r_angle_other_deg1.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.217
r_dihedral_angle_4_deg15.976
r_dihedral_angle_3_deg12.448
r_dihedral_angle_1_deg6.043
r_mcangle_it3.559
r_scbond_it2.77
r_mcbond_it2.268
r_mcbond_other2.268
r_angle_refined_deg1.497
r_angle_other_deg1.009
r_chiral_restr0.134
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3676
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4-AUTOMRphasing