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PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF848
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.36 α = 90 b = 80.36 β = 90 c = 139.56 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 2016-04-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 69.59 100 0.122 0.125 0.028 1 17.2 19.3 46059
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 1.51 100 2.553 2.627 0.615 0.532 18 3334
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 FOURIER SYNTHESIS THROUGHOUT 3DAI 1.47 69.59 43644 2343 99.97 0.172 0.1712 0.1871 0.2 RANDOM 23.011
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] 0.01 0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.473 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 4.496 r_mcangle_it 2.694 r_angle_refined_deg 1.825 r_mcbond_other 1.495 r_mcbond_it 1.481 r_angle_other_deg 1.44 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.473 r_dihedral_angle_4_deg 18.743 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_1_deg 4.496 r_mcangle_it 2.694 r_angle_refined_deg 1.825 r_mcbond_other 1.495 r_mcbond_it 1.481 r_angle_other_deg 1.44 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 224 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing