5A3N

Crystal structure of human PLU-1 (JARID1B) in complex with KDOAM25a


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 = 141.874α = 90
b = 141.874β = 90
c = 151.865γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
1219.8199.30.0821.712.6607153.5
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)
122.1195.80.643.58.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 51AF2122.8757644301899.140.183820.182810.20335RANDOM36.565
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]
0.430.210.43-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.71
r_dihedral_angle_4_deg14.753
r_dihedral_angle_3_deg12.656
r_dihedral_angle_1_deg6.204
r_mcangle_it3.228
r_scbond_it2.476
r_mcbond_other2.024
r_mcbond_it2.023
r_angle_refined_deg1.358
r_angle_other_deg0.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.71
r_dihedral_angle_4_deg14.753
r_dihedral_angle_3_deg12.656
r_dihedral_angle_1_deg6.204
r_mcangle_it3.228
r_scbond_it2.476
r_mcbond_other2.024
r_mcbond_it2.023
r_angle_refined_deg1.358
r_angle_other_deg0.947
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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_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 Atoms3656
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4-AUTOMRphasing