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Crystal structure of PprA from Deinococcus radiodurans in complex with DNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 1.0 ul of pre-incubated protein-DNA solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution.
| Protein-DNA solution: 5.0 mg/mL PprA (168 uM), dsDNA (100 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2.
| Crystallization solution (Molecular Dimensions - Morpheus 2 #2-18): 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4- hydroxy-L-proline,
0.1M BES, Triethanolamine (TEA), pH 7.5, 12.5% w/v PEG 4000, 20% w/v 1,2,6- Hexanetriol.
| Well solution: 1.5 M Ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.71 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.427 α = 90 b = 100.427 β = 90 c = 255.598 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 PILATUS 6M IMCA-CAT default optics (July 2018) 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.979280 APS 17-ID
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 5.79 86.972 90 0.119 0.123 0.03 0.999 13.5 16.6 4112 354.48
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 5.79 6.086 34.2 3.455 3.561 0.856 0.5 1.1 16.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 5.79 35.95 1.35 4083 197 90.65 0.272 0.2708 0.2992 0.2971 0.3431 573.79
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 16.0622 f_angle_d 0.6424 f_chiral_restr 0.0444 f_plane_restr 0.013 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8144 Nucleic Acid Atoms 615 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement JDirector data collection autoPROC data processing XDS data reduction Aimless data scaling pointless data scaling PHENIX phasing