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Structure of the catalytic domain of tankyrase 1 in complex with veliparib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 Buffer: 0.1 M Sodium Citrate (pH 5.60)
Salt: 1.0 M ammonium formate
Precipitant: 23.0 %w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.19 α = 90 b = 159.1 β = 90 c = 84.27 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 PIXEL DECTRIS PILATUS3 S 6M 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 79.55 92.8 0.999 19.1 6.4 110379
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 1.59 1.7 0.786
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 2rf5 1.59 79.55 110379 5532 79.5 0.205 0.204 0.1965 0.23 0.2178 RANDOM 30.17
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] 0.0892 -0.1857 0.0965
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.51 t_omega_torsion 3.98 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.51 t_omega_torsion 3.98 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 6651 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 76
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing autoPROC data reduction