5L3E

LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.3 M Na/K Tartrate, 100 mM ADA
Crystal Properties
Matthews coefficientSolvent content
82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.57α = 90
b = 178.4β = 90
c = 233.78γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

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
12.898.5799.80.1340.9948.3560074
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)
12.82.8799.41.3771.15.1

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 REPLACEMENTTHROUGHOUT2V1D2.898.5758908116599.690.200940.200460.22447RANDOM72.636
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]
6.7-3.94-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg16.198
r_dihedral_angle_3_deg14.647
r_long_range_B_refined12.198
r_long_range_B_other12.198
r_scangle_other9.292
r_mcangle_it7.86
r_mcangle_other7.86
r_dihedral_angle_1_deg6.519
r_scbond_it5.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_4_deg16.198
r_dihedral_angle_3_deg14.647
r_long_range_B_refined12.198
r_long_range_B_other12.198
r_scangle_other9.292
r_mcangle_it7.86
r_mcangle_other7.86
r_dihedral_angle_1_deg6.519
r_scbond_it5.899
r_scbond_other5.898
r_mcbond_it5.164
r_mcbond_other5.162
r_angle_refined_deg1.789
r_angle_other_deg1.019
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6293
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms229

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing