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human Artemis/SNM1C catalytic domain, crystal form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model from a SAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.69 α = 90 b = 111.01 β = 90 c = 55.16 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 S 6M 2019-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 1.97 35 99.6 0.05 16 6.4 32168
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 1.97 2.02 0.828
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 Model from a SAD data 1.97 34.541 32125 1560 99.526 0.22 0.2177 0.2247 0.2695 0.2743 53.457
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] 1.872 -0.993 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 17.477 r_dihedral_angle_1_deg 7.286 r_lrange_it 6.098 r_lrange_other 6.068 r_scangle_it 3.521 r_scangle_other 3.521 r_mcangle_other 2.847 r_mcangle_it 2.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 17.477 r_dihedral_angle_1_deg 7.286 r_lrange_it 6.098 r_lrange_other 6.068 r_scangle_it 3.521 r_scangle_other 3.521 r_mcangle_other 2.847 r_mcangle_it 2.846 r_scbond_it 2.17 r_scbond_other 2.17 r_mcbond_it 1.825 r_mcbond_other 1.814 r_angle_refined_deg 1.499 r_angle_other_deg 1.241 r_nbd_other 0.222 r_nbd_refined 0.201 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.153 r_metal_ion_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2911 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing