5L3B

Human LSD1/CoREST: LSD1 D556G mutation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298Tartrate 1-1.4 M, ADA 100 mM pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.2882

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.088α = 90
b = 179.122β = 90
c = 234.411γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97626ESRFID23-1

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
13.35099.60.1310.9887.23.837869
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)
13.33.4599.60.6131.73.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2V1D3.3503712974099.360.194830.194550.20783RANDOM85.175
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]
8.41-4.31-4.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.832
r_dihedral_angle_3_deg18.058
r_dihedral_angle_4_deg15.182
r_long_range_B_refined9.327
r_long_range_B_other9.327
r_mcangle_other6.539
r_mcangle_it6.538
r_scangle_other6.498
r_dihedral_angle_1_deg5.622
r_mcbond_it4.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.832
r_dihedral_angle_3_deg18.058
r_dihedral_angle_4_deg15.182
r_long_range_B_refined9.327
r_long_range_B_other9.327
r_mcangle_other6.539
r_mcangle_it6.538
r_scangle_other6.498
r_dihedral_angle_1_deg5.622
r_mcbond_it4.107
r_mcbond_other4.103
r_scbond_it3.9
r_scbond_other3.899
r_angle_refined_deg1.308
r_angle_other_deg0.917
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms6289
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing