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Crystal structure of the BIR3 - SERK2 complex from Arabidopsis thaliana.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FG8 6fg8, 4z61 experimental model PDB 4Z61 6fg8, 4z61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 25% (w/v) PEG 3,350, 0.2 M MgCl_2 x 6H_2O, 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.184 α = 90 b = 52.155 β = 90 c = 308.892 γ = 90
Symmetry Space Group P 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 2M-F 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000027 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 49.41 99.9 0.111 0.115 0.999 17 13 42439 -3 54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 99.7 1.604 1.67 0.71 1.4 13
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 MOLECULAR REPLACEMENT THROUGHOUT 6fg8, 4z61 2.2 49.41 40314 2122 99.93 0.21852 0.21698 0.2209 0.2481 0.2479 RANDOM 61.234
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] 1.21 1.96 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.427 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 13.17 r_long_range_B_refined 6.071 r_long_range_B_other 6.068 r_dihedral_angle_1_deg 5.957 r_scangle_other 2.785 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scbond_it 1.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.427 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 13.17 r_long_range_B_refined 6.071 r_long_range_B_other 6.068 r_dihedral_angle_1_deg 5.957 r_scangle_other 2.785 r_mcangle_it 1.977 r_mcangle_other 1.976 r_scbond_it 1.668 r_scbond_other 1.668 r_angle_refined_deg 1.434 r_mcbond_it 1.214 r_mcbond_other 1.214 r_angle_other_deg 0.808 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5634 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing