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Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 58.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.444 α = 90 b = 98.544 β = 96.08 c = 101.358 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 CCD ADSC QUANTUM 315 2012-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97923 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.65 50 98.8 0.072 0.054 31359 30975 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 99.9 0.95 0.9 2.2 4.6 1509
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4FWE 2.7 50 3 3 31359 26437 1360 93.18 0.20705 0.20705 0.20554 0.2049 0.23694 0.2063 RANDOM 41.283
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] 0.14 0.14 0.4 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 18.202 r_dihedral_angle_1_deg 5.727 r_angle_refined_deg 1.228 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 18.202 r_dihedral_angle_1_deg 5.727 r_angle_refined_deg 1.228 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 5737 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 56
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling