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Crystal structure of PprA filament from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MC8 PDB entry 6MC8 chain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine trihydrochloride, 1,4-diaminobutane dihydrochloride, DL-ornithine monohydrochloride), 50% v/v Precipitant Mix 6 (25% w/v PEG4000, 40% w/v 1,2,6-hexanetriol), 0.1 M Buffer System 4 (Gly-Gly, AMPD) at pH 6.5. The drop was suspended over a 1.5 M ammonium sulfate dehydrating solution and incubated at 20 degrees C for about 5 months.
Crystal Properties Matthews coefficient Solvent content 4.55 72.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.979 α = 90 b = 148.979 β = 90 c = 79.25 γ = 120
Symmetry Space Group P 64 2 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 CCD RIGAKU SATURN 944+ 2018-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 5.94 67.53 98.8 0.261 0.278 0.074 0.995 9.5 13.9 1513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 5.94 6.64 96.8 0.565 0.496 1.4 13.8
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 PDB entry 6MC8 chain B 5.94 50.0319 1.34 1502 74 98.62 0.2881 0.2871 0.288 0.3088 0.3203
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 7.704 f_angle_d 0.357 f_chiral_restr 0.036 f_plane_restr 0.002 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1473 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing StructureStudio data collection