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Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 289 21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.691 α = 90 b = 96.273 β = 90 c = 182.797 γ = 90
Symmetry Space Group C 2 2 21
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 270 2012-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 0.97943 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.13 50 93.9 10.2 47400 44518 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 2.13 2.17 85.6 0.889 0.663 2.2 6.6 1987
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 4FWJ 2.13 50 3 3 47400 41665 2114 93.98 0.20486 0.20486 0.20283 0.2027 0.24556 0.201 RANDOM 49.419
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] 1.47 1.24 -2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.805 r_dihedral_angle_3_deg 17.573 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.359 r_chiral_restr 0.11 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.805 r_dihedral_angle_3_deg 17.573 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.359 r_chiral_restr 0.11 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 5845 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 69
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling