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Crystal Structure of PriB Binary Complex with Product Diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5INJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM daptomycin and 1 mM Dimethylallyl diphosphate (DMAPP) with reservoir solution containing 0.1 M Tris pH 8, 28% w/v PEG 4000. The mixed drops of 0.4 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark.
Crystal Properties Matthews coefficient Solvent content 1.9 35.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.727 α = 90 b = 83.02 β = 90 c = 95.304 γ = 90
Symmetry Space Group P 2 21 21
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 MX225HE 2015-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 38.224 99.71 0.14 8.59 1.9 101546
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 1.5 1.554 99.79 1.9 1.7 1.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5INJ 1.5 38.224 1.34 101416 3052 98.98 0.1945 0.1935 0.1948 0.227 0.2283 Random Selection 27.3616
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2663 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 29
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction