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PanDDA analysis group deposition of ground-state model of ATAD2
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 4.21 70.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.466 α = 90 b = 80.466 β = 90 c = 139.654 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 2M 2016-04-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.92819 Diamond I02
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 1.44 27.93 99.9 0.054 0.056 0.013 1 33.6 19.1 49175
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 1.44 1.48 99.1 0.726 0.749 0.183 0.915 16.4 3492
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 1.44 27.91 46610 2494 99.85 0.169 0.1686 0.1766 0.1861 RANDOM 20.166
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] 0.14 0.07 0.14 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.566 r_dihedral_angle_4_deg 13.751 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 4.835 r_mcangle_it 3.32 r_angle_refined_deg 2.384 r_mcbond_it 2.201 r_mcbond_other 2.188 r_angle_other_deg 1.453 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.566 r_dihedral_angle_4_deg 13.751 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 4.835 r_mcangle_it 3.32 r_angle_refined_deg 2.384 r_mcbond_it 2.201 r_mcbond_other 2.188 r_angle_other_deg 1.453 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 226 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing