6E1F | pdb_00006e1f

Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IT3PDB ENTRY 5IT3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.727.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.957α = 90
b = 57.514β = 90
c = 97.019γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2018-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
11.1635.1896.80.07250.711.494426
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.161.1986.40.5073.58.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5IT31.1635.1892362200096.80.1330.1330.130.1690.17RANDOM14.21
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]
-0.01-0.140.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.086
r_sphericity_free22.147
r_dihedral_angle_4_deg19.467
r_dihedral_angle_3_deg12.753
r_sphericity_bonded12.715
r_dihedral_angle_1_deg5.803
r_long_range_B_refined4.036
r_scangle_other3.988
r_long_range_B_other3.873
r_rigid_bond_restr3.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.086
r_sphericity_free22.147
r_dihedral_angle_4_deg19.467
r_dihedral_angle_3_deg12.753
r_sphericity_bonded12.715
r_dihedral_angle_1_deg5.803
r_long_range_B_refined4.036
r_scangle_other3.988
r_long_range_B_other3.873
r_rigid_bond_restr3.469
r_scbond_it3.335
r_scbond_other3.233
r_mcangle_it2.756
r_mcangle_other2.755
r_mcbond_it2.215
r_mcbond_other2.215
r_angle_refined_deg1.907
r_angle_other_deg1.192
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2885
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms10

Software

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