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Crystal structure of AtKAI2 in complex with KK181N1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.7 M sodium phosphate, pH 7.0, and 1% 1,2-butanediol
Crystal Properties Matthews coefficient Solvent content 3.43 64.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.314 α = 90 b = 64.042 β = 104.79 c = 114.958 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 4M 2020-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.08 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 43.54 99.4 0.108 0.128 0.068 0.993 7.8 3.5 94191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99.9 0.797 0.936 0.488 0.508 1.9 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4JYP 1.9 42.35 1.34 94154 4659 99.36 0.2409 0.2391 0.2391 0.2747 0.2748 31.01
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.0254 f_angle_d 0.8139 f_chiral_restr 0.0534 f_bond_d 0.0067 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6175 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing