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Crystal structure of human FTO in complex with small-molecule inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 10.0% (W/V) PEG 3350, 100 MM SODIUM
CITRATE, PH 5.6, 7% TERT-BUTANOL, 1 MM ZNSO4, 1 MM COMPOUND,
VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.77 α = 90 b = 141.77 β = 90 c = 83.751 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2013-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97 SSRF BL17U
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 2.8 70.89 97.3 14.4 5.4 14979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.96
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LFM 2.8 70.88 14231 748 97.3 0.211 0.209 0.253 0.2702 RANDOM 86.09
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] -0.37 -0.19 -0.37 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.887 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_4_deg 11.294 r_long_range_B_refined 7.582 r_long_range_B_other 7.581 r_dihedral_angle_1_deg 5.845 r_mcangle_it 4.835 r_mcangle_other 4.834 r_scangle_other 4.573 r_mcbond_it 2.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.887 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_4_deg 11.294 r_long_range_B_refined 7.582 r_long_range_B_other 7.581 r_dihedral_angle_1_deg 5.845 r_mcangle_it 4.835 r_mcangle_other 4.834 r_scangle_other 4.573 r_mcbond_it 2.963 r_mcbond_other 2.961 r_scbond_it 2.716 r_scbond_other 2.715 r_angle_refined_deg 1.125 r_angle_other_deg 0.908 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3341 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose iMOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement