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SMYD2 in complex with small molecule inhibitor compound-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TG5 PDB ENTRY 3TG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 SMYD2 CO-CRYSTALLIZED WITH 2 MMOL SAM. RESERVOIR 23% PEG 3350, 100 MMOL HEPES PH 7.0. CO-COMPLEX WITH INHIBITOR FORMED BY SOAKING SMYD2-SAM CRYSTALS WITH 5 MILLIMOLAR COMPOUND-2 FOR 1 HOUR. CRYO WITH ADDITIONAL 20% GLYCEROL AND 1 MMOL COMPOUND-2.
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.493 α = 90 b = 51.759 β = 90 c = 69.568 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2013-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.92 48.11 97.9 0.08 12.83 3.69 36156
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 1.92 2.03 97.4 0.7 2.3
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 PDB ENTRY 3TG5 1.92 47.59 34348 1808 97.94 0.25958 0.25747 0.2503 0.30052 0.2952 RANDOM 52.97
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] -0.22 0.32 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_4_deg 16.685 r_dihedral_angle_1_deg 7.438 r_angle_other_deg 3.631 r_scbond_it 2.336 r_angle_refined_deg 1.986 r_mcangle_it 1.854 r_mcbond_it 1.255 r_mcbond_other 1.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.701 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_4_deg 16.685 r_dihedral_angle_1_deg 7.438 r_angle_other_deg 3.631 r_scbond_it 2.336 r_angle_refined_deg 1.986 r_mcangle_it 1.854 r_mcbond_it 1.255 r_mcbond_other 1.253 r_chiral_restr 0.111 r_gen_planes_other 0.019 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3419 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing