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SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket
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 MICROBATCH 298 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.34 α = 90 b = 147.325 β = 114.64 c = 98.537 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 DECTRIS PILATUS 6M 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 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 2.2 50 98.1 0.123 0.997 7 2.9 110334
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 2.2 2.24 98.2 0.252 0.8 2.8
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 2.2 50 104740 5562 96.62 0.19205 0.1901 0.1961 0.228 0.2305 RANDOM 42.431
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] 1.05 0.11 -2.39 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.387 r_dihedral_angle_3_deg 17.41 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_1_deg 6.155 r_long_range_B_refined 6.03 r_long_range_B_other 6.019 r_scangle_other 3.495 r_mcangle_it 2.531 r_mcangle_other 2.531 r_scbond_other 2.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.387 r_dihedral_angle_3_deg 17.41 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_1_deg 6.155 r_long_range_B_refined 6.03 r_long_range_B_other 6.019 r_scangle_other 3.495 r_mcangle_it 2.531 r_mcangle_other 2.531 r_scbond_other 2.116 r_scbond_it 2.115 r_angle_refined_deg 2.03 r_mcbond_it 1.538 r_mcbond_other 1.536 r_angle_other_deg 1.118 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.004 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 15690 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 372
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing