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Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B0T PDB ENTRY 4B0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 100 MM MES, PH 6.8 (RT), 150 - 200 MM SODIUM TARTRATE, 2 - 4 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.52 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.84 α = 90 b = 84.02 β = 90 c = 215.11 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2012-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.8 39 99.8 0.11 11.8 4.9 29211 2.44 50.66
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 2.8 2.85 99.8 0.67 2.44 4.8
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 4B0T 2.8 39.131 1.35 29211 1490 99.62 0.2149 0.2131 0.2144 0.2475 0.2497
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 15.434 f_angle_d 1.118 f_chiral_restr 0.063 f_bond_d 0.012 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7772 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing