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Human SIRT6 crystal structure in complex with ADP ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 297 2M NH4SO4, 2%PEG400, 0.1M BIS-TRIS pH5.8, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.367 α = 118.09 b = 90.2 β = 91.39 c = 90.18 γ = 115.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2009-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97945 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.03 50 98.2 0.119 0.119 14.6 4.5 118501 118501 29.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.07 97 0.956 0.956 1.7 4.1 5734
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3K35 2.04 29.87 115679 5783 0.1842 0.1827 0.2131 0.2082 RANDOM 33.39
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] -5.4528 5.9642 2.7355 -1.1849 1.976 6.6377
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.13 t_omega_torsion 2.48 t_angle_deg 0.94 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.13 t_omega_torsion 2.48 t_angle_deg 0.94 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12761 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 363
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing BUSTER refinement HKL-3000 data reduction HKL-3000 data scaling