2V1D

Structural basis of LSD1-CoREST selectivity in histone H3 recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IW5PDB ENTRY 2IW5

Crystallization

Crystal Properties
Matthews coefficientSolvent content
780

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.057α = 90
b = 180.496β = 90
c = 233.387γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
13.150960.1111.44.244088
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)
13.13.2798.10.511.94.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2IW53.176.034322486095.20.2240.2230.239RANDOM84.85
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]
6.79-4.24-2.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.413
r_dihedral_angle_3_deg21.988
r_dihedral_angle_4_deg19.234
r_dihedral_angle_1_deg6.933
r_scangle_it2.998
r_scbond_it1.71
r_angle_refined_deg1.67
r_mcangle_it1.503
r_mcbond_it0.831
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.413
r_dihedral_angle_3_deg21.988
r_dihedral_angle_4_deg19.234
r_dihedral_angle_1_deg6.933
r_scangle_it2.998
r_scbond_it1.71
r_angle_refined_deg1.67
r_mcangle_it1.503
r_mcbond_it0.831
r_nbtor_refined0.328
r_symmetry_hbond_refined0.309
r_nbd_refined0.263
r_symmetry_vdw_refined0.257
r_xyhbond_nbd_refined0.172
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms6407
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing