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Crystal structure of human legumain (AEP) in complex with compound 11b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22 % PEG 3350, 0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.34 α = 90 b = 75.19 β = 90 c = 171.93 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 PILATUS3 2M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 36.73 95.8 0.12 2.3 3.7 36949
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 96.5 0.54 2.3 3.4
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 4AWA 2 36.71 35022 1853 94.6 0.223 0.222 0.2262 0.252 0.2527 RANDOM 27.4
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] -0.37 -1.51 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_4_deg 11.626 r_dihedral_angle_1_deg 5.459 r_long_range_B_refined 3.266 r_long_range_B_other 3.154 r_mcangle_it 1.418 r_mcangle_other 1.418 r_scangle_other 1.318 r_angle_refined_deg 1.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_4_deg 11.626 r_dihedral_angle_1_deg 5.459 r_long_range_B_refined 3.266 r_long_range_B_other 3.154 r_mcangle_it 1.418 r_mcangle_other 1.418 r_scangle_other 1.318 r_angle_refined_deg 1.026 r_angle_other_deg 0.894 r_mcbond_it 0.794 r_mcbond_other 0.793 r_scbond_it 0.758 r_scbond_other 0.758 r_chiral_restr 0.088 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 4206 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing