5FP3

Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1M TRIS HCL, BICINE PH 8.5, 37.5% MPD, PEG1K, PEG3350, 0.03M MGCL2, 0.03M CACL2
Crystal Properties
Matthews coefficientSolvent content
2.2946.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.199α = 85.59
b = 65.552β = 67.65
c = 77.301γ = 68.39
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002010-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRF

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
12.0540960.0711.42.1616152
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)
12.052.0990.30.322.22

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 REPLACEMENTTHROUGHOUTNONE2.0571.359141247095.70.206220.204640.24322RANDOM25.083
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]
0.11-2.17-1.271.893.030.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.377
r_dihedral_angle_3_deg10.313
r_dihedral_angle_4_deg8.036
r_dihedral_angle_1_deg4.467
r_angle_refined_deg0.818
r_angle_other_deg0.73
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.377
r_dihedral_angle_3_deg10.313
r_dihedral_angle_4_deg8.036
r_dihedral_angle_1_deg4.467
r_angle_refined_deg0.818
r_angle_other_deg0.73
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms6836
Nucleic Acid Atoms
Solvent Atoms835
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling