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Co-crystal structure of human SMYD1 in complex with MYH2 peptide and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 12.5 % (w/v) PEG 1K, 12.5 % (w/v) PEG 3350, 12.5 % (v/v) MPD, 0.03 M of each halide, 0.1 M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.53 65.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.082 α = 90 b = 154.433 β = 90 c = 181.067 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 EIGER2 X 16M 2022-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.76 50 99.9 0.092 0.099 0.037 0.996 7.2 7.2 64064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.81 100 0.974 1.05 0.387 0.722 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.76 47.55 63996 3304 99.3 0.196 0.194 0.1992 0.23 0.2356 RANDOM 74.9
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] -7.7279 1.9087 5.8192
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.94 t_omega_torsion 2.81 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.94 t_omega_torsion 2.81 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11083 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 87
Software Software Software Name Purpose BUSTER refinement HKL-3000 data scaling PHASER phasing