2UXN

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
Crystal Properties
Matthews coefficientSolvent content
679.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.949α = 90
b = 178.646β = 90
c = 234.93γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM2006-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-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
12.6948.5799.90.0536.69.969440-381.2
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)
12.692.7198.50.681.88.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.724966383150299.90.2420.2410.272RANDOM64.3
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]
6.3-3.64-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.073
r_dihedral_angle_3_deg16.083
r_dihedral_angle_4_deg14.126
r_scangle_it1.668
r_dihedral_angle_1_deg1.593
r_angle_refined_deg1.205
r_scbond_it0.923
r_mcangle_it0.875
r_mcbond_it0.508
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.073
r_dihedral_angle_3_deg16.083
r_dihedral_angle_4_deg14.126
r_scangle_it1.668
r_dihedral_angle_1_deg1.593
r_angle_refined_deg1.205
r_scbond_it0.923
r_mcangle_it0.875
r_mcbond_it0.508
r_nbtor_refined0.302
r_symmetry_hbond_refined0.198
r_nbd_refined0.192
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.118
r_chiral_restr0.081
r_bond_refined_d0.008
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 Atoms6337
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling