3FPD

G9a-like protein lysine methyltransferase inhibition by BIX-01294


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IGQPDB ENTRY 2IGQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52890.1 M HEPES pH 7.5, 18-20 % polyethylene glycol 4000 and 7-10 % isopropanol, in the absence or presence of DMSO (6-36%), VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.0159.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.3α = 90
b = 95.2β = 90
c = 101.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
12.430.2691.70.09710.34.426244-332.3
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)
2.42.510.4323.41995

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IGQ2.430.2624680120186.30.2210.262RANDOM39.8
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]
13.35-13.970.62
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.4
c_scangle_it2.9
c_mcangle_it2.27
c_scbond_it1.94
c_mcbond_it1.32
c_angle_deg1.3
c_improper_angle_d0.82
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4174
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms132

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling