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The structure of GTP-dTTP-bound SAMHD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000
, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.686 α = 90 b = 109.757 β = 122.8 c = 92.951 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS PILATUS 2M-F 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.10 Photon Factory BL-1A
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 2.2 50 100 0.065 19.1 6.8 65099 65099 1.5 1.5 40
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 2.2 2.24 100 0.637 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 4MZ7 2.2 50 1 1 61739 61677 3247 99.9 0.19503 0.19362 0.1988 0.222 0.2245 RANDOM 50.537
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] -2.64 -0.13 2.37 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 14.925 r_long_range_B_refined 6.831 r_long_range_B_other 6.826 r_dihedral_angle_1_deg 5.049 r_scangle_other 4.888 r_mcangle_it 3.751 r_mcangle_other 3.751 r_scbond_other 3.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 14.925 r_long_range_B_refined 6.831 r_long_range_B_other 6.826 r_dihedral_angle_1_deg 5.049 r_scangle_other 4.888 r_mcangle_it 3.751 r_mcangle_other 3.751 r_scbond_other 3.044 r_scbond_it 3.042 r_mcbond_it 2.436 r_mcbond_other 2.436 r_angle_refined_deg 1.304 r_angle_other_deg 0.937 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_gen_planes_refined 0.005 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 7968 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 182
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling