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Crystal structure of the Prp43-ADP-BeF3 complex (in hexagonal space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 40 % (v/v) pentaerythritol propoxylate (5/4 PO/OH), 6 % (v/v) ethanol, 16 % (v/v) glycerine and 100 mM Tris/HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.95 75.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.342 α = 90 b = 184.342 β = 90 c = 82.317 γ = 120
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-F 2015-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.24 92.171 98.8 0.098 0.998 14.65 4 25305 91.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.24 3.39 94.9 0.762 0.638 2.26 3.59
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 5LTA 3.241 92.171 1.35 25304 1919 98.87 0.1846 0.1821 0.1869 0.2166 0.2197
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 11.736 f_angle_d 0.672 f_chiral_restr 0.026 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5622 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing