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ATAD2 in complex with FragLite1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.298 α = 90 b = 79.298 β = 90 c = 137.846 γ = 120
Symmetry Space Group P 65 2 2
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 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.47 61.47 100 0.08 0.084 0.025 0.999 16.6 20.1 44319
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 3.838 4.172 1.613 0.375 12.4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DAI 1.47 61.47 44243 2171 99.934 0.203 0.202 0.2304 0.2442 31.643
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] 0.048 0.024 0.048 -0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.554 r_lrange_it 19.327 r_lrange_other 19.321 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_4_deg 10.776 r_scangle_other 8.686 r_scangle_it 8.662 r_scbond_it 4.825 r_scbond_other 4.813 r_dihedral_angle_1_deg 4.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.554 r_lrange_it 19.327 r_lrange_other 19.321 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_4_deg 10.776 r_scangle_other 8.686 r_scangle_it 8.662 r_scbond_it 4.825 r_scbond_other 4.813 r_dihedral_angle_1_deg 4.422 r_mcangle_other 4.005 r_mcangle_it 3.995 r_mcbond_it 2.885 r_mcbond_other 2.87 r_angle_refined_deg 2.109 r_angle_other_deg 1.563 r_symmetry_nbd_refined 0.699 r_nbd_other 0.399 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.231 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.177 r_chiral_restr 0.103 r_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing