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ATAD2 in complex with FragLite2
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 = 79.163 α = 90 b = 79.163 β = 90 c = 138.226 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 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.976 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 1.5 61.42 96.8 0.077 0.081 0.024 0.999 18.2 19.9 40300
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 1.5 1.53 3.267 3.515 1.26 0.371 12.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DAI 1.5 61.42 40253 2057 96.525 0.199 0.1973 0.1967 0.2233 0.2223 32.315
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] 0.04 0.02 0.04 -0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.802 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_4_deg 13.562 r_lrange_other 11.668 r_lrange_it 11.629 r_scangle_other 7.577 r_scangle_it 7.559 r_scbond_it 5.244 r_scbond_other 5.241 r_dihedral_angle_1_deg 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.802 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_4_deg 13.562 r_lrange_other 11.668 r_lrange_it 11.629 r_scangle_other 7.577 r_scangle_it 7.559 r_scbond_it 5.244 r_scbond_other 5.241 r_dihedral_angle_1_deg 4.61 r_mcangle_it 4.203 r_mcangle_other 4.2 r_mcbond_it 2.955 r_mcbond_other 2.952 r_angle_refined_deg 1.993 r_angle_other_deg 1.527 r_symmetry_nbd_refined 0.535 r_nbd_refined 0.515 r_xyhbond_nbd_refined 0.38 r_nbd_other 0.355 r_symmetry_nbd_other 0.292 r_symmetry_xyhbond_nbd_refined 0.26 r_symmetry_xyhbond_nbd_other 0.222 r_nbtor_refined 0.178 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_xyhbond_nbd_other 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing