5H6Q

Crystal structure of LSD1-CoREST in complex with peptide 11


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M N-(2-Acetamido) iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.825α = 90
b = 180.488β = 90
c = 233.375γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2015-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.534099.80.06329.57.584828-3
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)
12.532.5797.80.8570.8572.17

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 REPLACEMENTTHROUGHOUT2V1D2.534083140168699.750.224560.224120.24675RANDOM71.324
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]
6.12-5.62-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.747
r_dihedral_angle_4_deg17.627
r_dihedral_angle_3_deg15.33
r_long_range_B_refined10.343
r_long_range_B_other10.343
r_scangle_other7.854
r_mcangle_it7.106
r_mcangle_other7.105
r_dihedral_angle_1_deg5.957
r_scbond_it4.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.747
r_dihedral_angle_4_deg17.627
r_dihedral_angle_3_deg15.33
r_long_range_B_refined10.343
r_long_range_B_other10.343
r_scangle_other7.854
r_mcangle_it7.106
r_mcangle_other7.105
r_dihedral_angle_1_deg5.957
r_scbond_it4.946
r_scbond_other4.945
r_mcbond_it4.615
r_mcbond_other4.615
r_angle_refined_deg1.418
r_angle_other_deg0.937
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms6266
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
MOLREPphasing