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SAMHD1 HD domain bound to decitabine triphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 SPG buffer, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.492 α = 90 b = 146.536 β = 114.61 c = 98.552 γ = 90
Symmetry Space Group P 1 21 1
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 PSI PILATUS 6M 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.14 50 98.9 0.132 0.993 9.3 4.1 125515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 0.175 0.88
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 4BZB 2.14 50 119197 6373 97.98 0.17614 0.17354 0.1772 0.22534 0.2295 RANDOM 41.374
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] 0.59 0.31 -1.28 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.371 r_dihedral_angle_3_deg 16.84 r_dihedral_angle_4_deg 15.049 r_long_range_B_other 8.042 r_long_range_B_refined 8.041 r_scangle_other 6.38 r_dihedral_angle_1_deg 6.152 r_mcangle_it 4.576 r_mcangle_other 4.576 r_scbond_other 4.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.371 r_dihedral_angle_3_deg 16.84 r_dihedral_angle_4_deg 15.049 r_long_range_B_other 8.042 r_long_range_B_refined 8.041 r_scangle_other 6.38 r_dihedral_angle_1_deg 6.152 r_mcangle_it 4.576 r_mcangle_other 4.576 r_scbond_other 4.071 r_scbond_it 4.069 r_mcbond_it 3.055 r_mcbond_other 3.054 r_angle_refined_deg 1.86 r_angle_other_deg 1.034 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 15724 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing