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Crystal structure of oxidized legumain in complex with cystatin E/M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AW9 PDB ENTRIES 4AW9 AND 4N6L experimental model PDB 4N6L PDB ENTRIES 4AW9 AND 4N6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 25% PEG 4000,
100 mM MES pH 6.5,
200 mM potassium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.61 α = 90 b = 85.75 β = 94.63 c = 58.95 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 CCD ADSC QUANTUM 315r 2013-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.87 48.47 97.7 35804 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 90.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRIES 4AW9 AND 4N6L 1.87 44.5 2 35804 34006 1778 97.55 0.21393 0.2136 0.21364 0.2187 0.21937 0.2229 RANDOM 21.562
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] -0.07 0.72 -0.79 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.084 r_dihedral_angle_4_deg 16.292 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 5.622 r_long_range_B_refined 2.983 r_long_range_B_other 2.685 r_angle_refined_deg 0.983 r_mcangle_it 0.837 r_mcangle_other 0.836 r_angle_other_deg 0.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.084 r_dihedral_angle_4_deg 16.292 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 5.622 r_long_range_B_refined 2.983 r_long_range_B_other 2.685 r_angle_refined_deg 0.983 r_mcangle_it 0.837 r_mcangle_other 0.836 r_angle_other_deg 0.674 r_scangle_other 0.621 r_mcbond_it 0.447 r_mcbond_other 0.447 r_scbond_it 0.34 r_scbond_other 0.339 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3026 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 72
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement iMOSFLM data reduction SCALA data scaling