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Human LSD1/CoREST: LSD1 D556G mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Tartrate 1-1.4 M, ADA 100 mM pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.28 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.088 α = 90 b = 179.122 β = 90 c = 234.411 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 300K 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97626 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.3 50 99.6 0.131 0.988 7.2 3.8 37869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.45 99.6 0.613 1.7 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2V1D 3.3 50 37129 740 99.36 0.19483 0.19455 0.2014 0.20783 0.2163 RANDOM 85.175
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_3_deg 18.058 r_dihedral_angle_4_deg 15.182 r_long_range_B_refined 9.327 r_long_range_B_other 9.327 r_mcangle_other 6.539 r_mcangle_it 6.538 r_scangle_other 6.498 r_dihedral_angle_1_deg 5.622 r_mcbond_it 4.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_3_deg 18.058 r_dihedral_angle_4_deg 15.182 r_long_range_B_refined 9.327 r_long_range_B_other 9.327 r_mcangle_other 6.539 r_mcangle_it 6.538 r_scangle_other 6.498 r_dihedral_angle_1_deg 5.622 r_mcbond_it 4.107 r_mcbond_other 4.103 r_scbond_it 3.9 r_scbond_other 3.899 r_angle_refined_deg 1.308 r_angle_other_deg 0.917 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 6289 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing