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Crystal structure of prenyltransferase AmbP1 pH8 complexed with GSPP and cis-indolyl vinyl isonitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM MES, 0.2M MgCl2, 22% PEG8000, ligands were soaked at pH8.0
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.267 α = 90 b = 117.267 β = 90 c = 49.324 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2017-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0000 NSRRC TPS 05A
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 1.999 49.3 99.7 0.052 0.999 19.6 7.4 45762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98.1 0.583 3.4 7
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 5Z43 1.999 37.745 1.36 45733 2016 99.81 0.1909 0.1889 0.1916 0.2352 0.2376
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 15.839 f_angle_d 0.911 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing