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PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with JKH93A
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 = 80.966 α = 90 b = 80.966 β = 90 c = 140.151 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 2016-04-26 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 1.54 28.04 99.8 0.064 0.066 0.015 1 31.8 19.2 40499
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 1.54 1.58 97.3 0.81 0.832 0.189 0.917 18.6 2869
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 FOURIER SYNTHESIS THROUGHOUT 3DAI 1.54 28.06 38399 2033 99.75 0.1631 0.1626 0.2105 0.1724 0.2144 RANDOM 23.401
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] 0.32 0.16 0.32 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.29 r_dihedral_angle_4_deg 19.174 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.469 r_mcangle_it 2.867 r_angle_refined_deg 1.962 r_mcbond_other 1.652 r_mcbond_it 1.617 r_angle_other_deg 1.514 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.29 r_dihedral_angle_4_deg 19.174 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.469 r_mcangle_it 2.867 r_angle_refined_deg 1.962 r_mcbond_other 1.652 r_mcbond_it 1.617 r_angle_other_deg 1.514 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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 219 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing