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Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1 ul of protein at 4.6mg/ml in 15mM Hepes pH7.5, 150mM NaCl, 20mM DTT were mixed with 1 ul reservoir (0.2M Ammonium sulfate, 0.1M MES pH6.5, 24% PEG 3350) and equilibrated against 80 ul reservoir
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.622 α = 90 b = 79.682 β = 90 c = 146.297 γ = 90
Symmetry Space Group I 21 21 21
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 KB Mirrors 2019-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.0722 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.558 73.148 91.3 0.123 0.129 0.995 12.8 12.3 12755 76.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.558 2.747 41.8 2.67 0.448
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.56 56.32 1.34 12733 616 82.74 0.2221 0.2198 0.2208 0.266 0.2645 87.34
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 23.7767 f_angle_d 0.6413 f_chiral_restr 0.0401 f_plane_restr 0.0041 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2262 Nucleic Acid Atoms 489 Solvent Atoms 28 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection autoPROC data processing PHENIX phasing Coot model building autoPROC data reduction autoPROC data scaling