☰ Navigation Tabs
The structure of Agmatinase from E. Coli at 3.2 A displaying guanidine in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Protein at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl. Crystallization: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.028 α = 90 b = 129.028 β = 90 c = 88.29 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS EIGER X 16M 2019-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.771 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.2 64.51 99.87 0.1561 0.1582 26.7 39.4 14314 84.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.314 100 0.1561 0.1582
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 3NPI 3.2 64.51 1.34 27100 1254 99.88 0.1741 0.1719 0.1759 0.2178 0.2217 81.5
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 17.8507 f_angle_d 1.3997 f_chiral_restr 0.0795 f_bond_d 0.0117 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6517 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling BALBES phasing