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Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.5 M ammonium sulfate, 1 M Lithium sulfate and 0.1 M trisodium citrate
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.465 α = 90 b = 170.465 β = 90 c = 196.515 γ = 90
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-F 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.949998 ESRF ID30B
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 2.01 49.69 90.2 0.12 0.08 0.99 6.8 2.8 337197 31.21
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 2.01 2.04 1.4 0.99 0.22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5nij 2.01 49.68 1.33 336594 17034 90.11 0.2091 0.2086 0.2113 0.2186 0.2214 36
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 14.5135 f_angle_d 1.1483 f_chiral_restr 0.5741 f_bond_d 0.006 f_plane_restr 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39208 Nucleic Acid Atoms Solvent Atoms 2254 Heterogen Atoms 679
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing