6H4W

Crystal structure of human KDM4A in complex with compound 19d


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Crystal Properties
Matthew coefficientSolvent content
2.4549.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.557α = 90
b = 101.487β = 99.07
c = 142.308γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2017-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.5419

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.8148.921000.3840.9427.58.53955567.24
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.812.921001.960.3810.97.6

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 REPLACEMENTTHROUGHOUT2oq72.8148.9239428201699.70.220.2180.266RANDOM53.96
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]
17.06317.6741-10.6653-6.3978
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.35
t_omega_torsion2.86
t_angle_deg1.11
t_bond_d0.01
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion20.35
t_omega_torsion2.86
t_angle_deg1.11
t_bond_d0.01
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
t_dihedral_angle_d
t_trig_c_planes
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10534
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms135

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing