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Crystal structure of KAI2 S95C mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HRX Arabidopsis thaliana
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 2.2 M ammonium sulfate, 1 M HEPES pH 7.2; KAI2 protein at 14 mg/mL, 1mM dGR24^(ent-5DS) ligand in DMSO
Crystal Properties Matthews coefficient Solvent content 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.798 α = 90 b = 55.869 β = 116.02 c = 53.147 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 16M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9464 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.51 47.76 99.3 0.118 0.073 0.998 8.2 6.9 41446
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 86.5 1.353 0.844 0.466 0.9 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.51 47.76 39292 2136 99.28 0.15736 0.15579 0.1675 0.18622 0.1989 RANDOM 19.061
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] 0.52 0.13 -0.59 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.506 r_long_range_B_refined 6.349 r_long_range_B_other 6.222 r_scangle_other 5.371 r_dihedral_angle_2_deg 5.221 r_scbond_it 3.648 r_scbond_other 3.646 r_mcangle_other 2.818 r_mcangle_it 2.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.506 r_long_range_B_refined 6.349 r_long_range_B_other 6.222 r_scangle_other 5.371 r_dihedral_angle_2_deg 5.221 r_scbond_it 3.648 r_scbond_other 3.646 r_mcangle_other 2.818 r_mcangle_it 2.813 r_mcbond_it 1.847 r_mcbond_other 1.839 r_angle_refined_deg 1.683 r_angle_other_deg 0.56 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2077 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing