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Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant
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 7.4 298 SPG buffer, PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.083 α = 90 b = 146.091 β = 115.03 c = 98.463 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 2015-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.8 50 98.7 0.194 0.199 0.099 3.2 6.9 54764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 99.7 0.736 0.333 7.1 2744
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 2.81 50 51938 2789 98.07 0.2101 0.208 0.2111 0.2477 0.2467 RANDOM 70.01
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] 0.08 1.59 -1.21 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.082 r_dihedral_angle_3_deg 20.365 r_dihedral_angle_4_deg 19.261 r_mcangle_it 4.93 r_dihedral_angle_1_deg 4.907 r_mcbond_it 3.134 r_mcbond_other 3.133 r_angle_refined_deg 1.487 r_angle_other_deg 1.425 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.082 r_dihedral_angle_3_deg 20.365 r_dihedral_angle_4_deg 19.261 r_mcangle_it 4.93 r_dihedral_angle_1_deg 4.907 r_mcbond_it 3.134 r_mcbond_other 3.133 r_angle_refined_deg 1.487 r_angle_other_deg 1.425 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15700 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 377
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing HKL-2000 data reduction