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LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor
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 6.5 298 100 mM ADA pH 6.5
1.2 M Na/Ka Tartrate
Crystal Properties Matthews coefficient Solvent content 6.22 80.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.13 α = 90 b = 179.59 β = 90 c = 234.18 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 2M 2015-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
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 99.85 100 0.191 0.943 5.7 5.3 38477
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 3.45 100 1.484 1.4 5.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2V1D 3.3 99.85 37697 751 99.86 0.23169 0.2313 0.2318 0.24989 0.2461 RANDOM 80.845
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] 5.33 -3.2 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.687 r_dihedral_angle_3_deg 16.14 r_dihedral_angle_4_deg 15.38 r_long_range_B_refined 7.847 r_long_range_B_other 7.847 r_dihedral_angle_1_deg 6.159 r_mcangle_it 3.463 r_mcangle_other 3.463 r_scangle_other 3.149 r_mcbond_it 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.687 r_dihedral_angle_3_deg 16.14 r_dihedral_angle_4_deg 15.38 r_long_range_B_refined 7.847 r_long_range_B_other 7.847 r_dihedral_angle_1_deg 6.159 r_mcangle_it 3.463 r_mcangle_other 3.463 r_scangle_other 3.149 r_mcbond_it 1.946 r_mcbond_other 1.943 r_scbond_it 1.707 r_scbond_other 1.707 r_angle_refined_deg 1.676 r_angle_other_deg 1.036 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 6293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing