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Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZUM PDB: 4ZUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/ml msAPAH Protein, 0.2 M calcium chloride dihydrate, 20% w/v PEG 3350, 1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.744 α = 90 b = 163.17 β = 94.44 c = 65.744 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2019-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.75 46.27 95.6 0.085 7.3 3.2 131376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 0.47
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB: 4ZUM 1.75 46.27 1.34 131376 6869 94.83 0.1765 0.1746 0.2116 0.2074
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 8.229 f_angle_d 0.839 f_chiral_restr 0.051 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10619 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing