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Crystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 286 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5)
Temperature(13), Well volume(500ul), 5uL of HCL (12.1M) was added to the reservoir drop prior to drop setup
Crystal Properties Matthews coefficient Solvent content 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.119 α = 90 b = 66.119 β = 90 c = 259.073 γ = 120
Symmetry Space Group P 65 2 2
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 ADSC QUANTUM 270 2016-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
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 2.1 50 95 0.087 4 10.6 19879
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 2.1 2.14 93 0.824 10.8
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 3KMA 2.1 45 18019 960 92.3 0.179 0.176 0.1891 0.239 0.2478 RANDOM 30.49
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 -0.07 -0.14 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_4_deg 12.454 r_long_range_B_refined 8.547 r_long_range_B_other 8.422 r_dihedral_angle_1_deg 7.037 r_scangle_other 6.039 r_mcangle_it 4.139 r_mcangle_other 4.137 r_scbond_it 3.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.057 r_dihedral_angle_3_deg 14.498 r_dihedral_angle_4_deg 12.454 r_long_range_B_refined 8.547 r_long_range_B_other 8.422 r_dihedral_angle_1_deg 7.037 r_scangle_other 6.039 r_mcangle_it 4.139 r_mcangle_other 4.137 r_scbond_it 3.833 r_scbond_other 3.719 r_mcbond_it 2.749 r_mcbond_other 2.738 r_angle_refined_deg 1.799 r_angle_other_deg 1.011 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 2013 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling Sir2014 phasing PHENIX model building