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Crystal structure of human legumain in complex with Gly-Ser-Asn peptide
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 4.5 293 22 % PEG 3350 and 0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.36 α = 90 b = 75.11 β = 90 c = 172.31 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 0.87290 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 57.44 99.5 0.11 0.99 9.6 4.2 45170 19.5305905593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 97.5 0.65 0.74
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 4awa 1.9 56.6157028198 1.3350264822 45086 2277 99.3608956276 0.193606631772 0.192251827999 0.193 0.219472983595 0.2202 22.3537685644
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 16.0865465895 f_angle_d 1.2368767116 f_chiral_restr 0.0894521101237 f_plane_restr 0.0129341744767 f_bond_d 0.00991304388315
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling PHENIX phasing