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The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine
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 4.2 291 Agmatinase at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl2.
Condition: 0.1 M phosphate/citrate pH 4.2 and 40% PEG 300
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.746 α = 90 b = 81.746 β = 90 c = 207.436 γ = 120
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 1.0332 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 1.8 35.79 99.87 0.06576 0.06753 28.76 19.9 25154 27.14
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 1.8 1.864 0.892 0.9161 3.61
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 1.8 35.79 1.34 25127 1244 99.89 0.1713 0.1701 0.1698 0.1947 0.1939 33.35
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 16.9009 f_angle_d 1.3536 f_chiral_restr 0.091 f_bond_d 0.0145 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2256 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling BALBES phasing Coot model building