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Crystal structure of PprA S-F filament from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9OM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 1.0 ul of protein solution was mixed with 2.0 uL of crystallization
solution and hung upside-down in a sealed chamber containing 1mL of well
solution. | Protein solution: 2.98 mg/mL PprA (100 uM), 150mM KCl,
20mM Tris, pH 7.5 | Crystallization solution: 800 mM LiCl, 32% (w/v) PEG
4000, 100 mM HEPES, pH 8.0 | Well solution: 0.8 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.425 α = 90 b = 147.348 β = 90 c = 44.473 γ = 90
Symmetry Space Group P 21 21 2
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 (December 2016) 2016-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97950 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 1.82 76.448 92.9 0.583 0.597 0.128 0.991 7.8 20.8 28051 17.7
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 1.82 2.383 81.6 3.74 3.842 0.864 0.615 2.6 17.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.82 44.47 1.34 28033 1407 52.32 0.2624 0.2617 0.2752 0.2777 27.2
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 15.6 f_angle_d 1.0833 f_chiral_restr 0.0485 f_plane_restr 0.0115 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose JDirector data collection autoPROC data processing XDS data reduction Aimless data scaling pointless data scaling PHASER phasing PHENIX refinement