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human Artemis/SNM1C catalytic domain, crystal form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.209 α = 90 b = 105.675 β = 90 c = 116.037 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 PILATUS3 S 6M 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0333 APS 23-ID-D
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 2.37 50 100 0.148 9.7 6.4 35315
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 2.37 2.43 0.784
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE SAD model 2.37 44.462 35218 1641 99.824 0.224 0.2207 0.2245 0.2803 0.2739 31.687
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] 1.37 -0.983 -0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.792 r_dihedral_angle_4_deg 19.064 r_dihedral_angle_3_deg 17.146 r_dihedral_angle_1_deg 7.168 r_lrange_it 5.196 r_lrange_other 5.183 r_scangle_it 3.443 r_scangle_other 3.442 r_mcangle_it 2.907 r_mcangle_other 2.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.792 r_dihedral_angle_4_deg 19.064 r_dihedral_angle_3_deg 17.146 r_dihedral_angle_1_deg 7.168 r_lrange_it 5.196 r_lrange_other 5.183 r_scangle_it 3.443 r_scangle_other 3.442 r_mcangle_it 2.907 r_mcangle_other 2.907 r_scbond_it 2.002 r_scbond_other 2.002 r_mcbond_it 1.743 r_mcbond_other 1.743 r_angle_refined_deg 1.33 r_angle_other_deg 1.139 r_nbd_other 0.21 r_nbd_refined 0.188 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.112 r_metal_ion_refined 0.088 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.013 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5770 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing