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ATAD2 in complex with FragLite28
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, HANGING DROP 6.5 293 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.068 α = 90 b = 79.068 β = 90 c = 137.07 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 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911 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 1.45 68.54 100 0.058 0.059 0.013 0.999 31.7 38 45657
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 1.45 1.47 5.476 5.652 1.39 0.364 31.3
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 1.45 68.54 45582 2317 99.971 0.209 0.2077 0.2157 0.2423 0.2448 34.054
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] -0.171 -0.085 -0.171 0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.891 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 15.192 r_lrange_it 9.132 r_lrange_other 9.129 r_scangle_it 7.128 r_scangle_other 7.124 r_scbond_it 5.02 r_scbond_other 5.016 r_dihedral_angle_1_deg 4.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.891 r_dihedral_angle_4_deg 15.653 r_dihedral_angle_3_deg 15.192 r_lrange_it 9.132 r_lrange_other 9.129 r_scangle_it 7.128 r_scangle_other 7.124 r_scbond_it 5.02 r_scbond_other 5.016 r_dihedral_angle_1_deg 4.612 r_mcangle_it 4.24 r_mcangle_other 4.237 r_mcbond_it 3.029 r_mcbond_other 3.026 r_angle_refined_deg 2.092 r_angle_other_deg 1.508 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.212 r_nbd_other 0.212 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.182 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_other 0.066 r_bond_refined_d 0.015 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 141 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing