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Crystal structure of the ANX2 ectodomain from Arabidopsis thaliana
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES pH 7.5, 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.566 α = 90 b = 41.766 β = 117.37 c = 93.371 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 2M-F 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999894 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 1.08 44.29 96.4 0.037 0.04 1 18.94 6.46 175203 -3 17.9
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 1.08 1.15 88.7 1.16 1.29 0.59 1.17 5.5
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 THROUGHOUT 1.08 44.29 165089 8689 96.13 0.16029 0.15911 0.1589 0.18269 0.1818 RANDOM 22.994
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] -0.91 0.88 -2.3 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_sphericity_free 34.505 r_dihedral_angle_4_deg 17.607 r_sphericity_bonded 14.466 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 3.911 r_long_range_B_other 3.436 r_rigid_bond_restr 2.736 r_scangle_other 2.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_sphericity_free 34.505 r_dihedral_angle_4_deg 17.607 r_sphericity_bonded 14.466 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_1_deg 6.568 r_long_range_B_refined 3.911 r_long_range_B_other 3.436 r_rigid_bond_restr 2.736 r_scangle_other 2.693 r_scbond_it 2.31 r_scbond_other 2.31 r_mcangle_other 2.123 r_mcangle_it 2.117 r_angle_refined_deg 1.714 r_mcbond_it 1.694 r_mcbond_other 1.686 r_angle_other_deg 1.045 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2950 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing