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Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic 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 7 277 35 % (v/v) MPD, 1.67 % (w/v) PEG 4000 and 100 mM Na HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.826 α = 90 b = 105.637 β = 90 c = 119.05 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-F 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.78 79.02 99.6 0.072 0.999 14.88 4.71 107277 27.3
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 1.78 1.89 98.8 1.235 0.619 1.64 4.66
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 1.78 67.986 1.35 107254 1957 99.6 0.177 0.1766 0.1831 0.1989 0.2038
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 13.727 f_angle_d 0.87 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5638 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing