☰ Navigation Tabs
Crystal structure of human legumain (AEP) in complex with compound 11
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 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.52 α = 90 b = 75.04 β = 90 c = 172.97 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 2.1 36.8 99.9 0.12 10.2 6 34046
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 2.1 2.17 99.8 0.82 2.8 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AWA 2.1 36.8 32251 1724 99.9 0.223 0.221 0.253 0.2382 RANDOM 28.34
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] 0.53 -1.72 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.246 r_dihedral_angle_4_deg 16.186 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 5.537 r_long_range_B_refined 3.569 r_long_range_B_other 3.446 r_mcangle_it 1.599 r_mcangle_other 1.599 r_scangle_other 1.534 r_angle_refined_deg 1.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.246 r_dihedral_angle_4_deg 16.186 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_1_deg 5.537 r_long_range_B_refined 3.569 r_long_range_B_other 3.446 r_mcangle_it 1.599 r_mcangle_other 1.599 r_scangle_other 1.534 r_angle_refined_deg 1.029 r_mcbond_it 0.905 r_mcbond_other 0.905 r_scbond_it 0.877 r_scbond_other 0.877 r_angle_other_deg 0.74 r_chiral_restr 0.061 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 253 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing