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Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 17.5 % polyethylene glycol 4,000, 250 mM (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.76 α = 97.7 b = 47.97 β = 102.72 c = 62.19 γ = 99.86
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 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000033 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 1.29 37.77 94.5 0.041 0.049 0.999 12.56 3.6 108820 -3
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 1.29 1.32 89.4 1.1 1.29 0.557 1.13 3.7
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 SAD THROUGHOUT 1.29 37.77 103379 5441 94.56 0.18762 0.18645 0.1957 0.20988 0.2148 RANDOM 23.415
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] 0.03 0.06 0.47 -0.51 -0.94 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_4_deg 20.81 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 6.311 r_long_range_B_refined 5.488 r_long_range_B_other 5.454 r_scangle_other 3.993 r_mcangle_it 2.983 r_mcangle_other 2.983 r_scbond_it 2.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_4_deg 20.81 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 6.311 r_long_range_B_refined 5.488 r_long_range_B_other 5.454 r_scangle_other 3.993 r_mcangle_it 2.983 r_mcangle_other 2.983 r_scbond_it 2.592 r_scbond_other 2.565 r_mcbond_it 1.889 r_mcbond_other 1.887 r_angle_refined_deg 1.502 r_angle_other_deg 1.083 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 3030 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHARP phasing