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Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound 2-hydroxyquinoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Crystals were grown in a MRC SD2 plate set with a TTP Labtech Mosquito crystallization robot. Protein sample at 9.2mg/mL was inclubated with 5mM 2-hydroxyquinoline at 293K for 1 hour prior to plate setup. The crystal providing the refinement data set was grown by mixing 200 nL protein-2HQ solution with 100 nL reservoir solution, 24% PEG3350, 0.2 M CaCl2, 0.1M bistris pH 6.5. Crystals were cryoprotected by soaking in reservoir solution supplemented to 30% PEG3350 and direct immersion in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.558 α = 90 b = 48.558 β = 90 c = 199.122 γ = 120
Symmetry Space Group P 32 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 9M 2020-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127230 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.71 33.19 99.31 0.1008 0.1036 0.02366 0.999 17.31 19.5 30590 27.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.771 98.19 1.421 1.458 0.323 0.964 1.65 20.2
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 7RIS 1.71 33.19 1.34 30523 1995 99.18 0.1794 0.1773 0.1763 0.2096 0.2084 37.04
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 13.3142 f_angle_d 1.0297 f_chiral_restr 0.0695 f_bond_d 0.0117 f_plane_restr 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2288 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing