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S. cerevisiae Prp43 in complex with RNA and ADPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 292 Crystallization buffer was prepared by mixing a solution containing 100 mM MES-NaOH, pH 6.0, 100 mM NaOAc, 8% PEG 10K and an additive solution (20% acetonitrile, 5% n-Dodecyl-?-D-maltoside) in a 5:1 (v:v).Microbatch drops were formed by mixing 1.8 ?l of the crystallization buffer with 1.2 ?l of the preformed complex
Crystal Properties Matthews coefficient Solvent content 2.86 57.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.063 α = 90 b = 154.031 β = 90 c = 78.988 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 CCD MARMOSAIC 225 mm CCD 2012-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.00 MAX II I911-3
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 4.2 30 99.5 0.255 0.99 8.67 6.05 15735 -3 121.22
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 4.2 4.34 99.9 1.054 2.08
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 3KX2 4.2 29.446 1.99 15493 1573 99.85 0.2629 0.2603 0.262 0.2861 0.2838
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 13.572 f_angle_d 0.567 f_chiral_restr 0.023 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12164 Nucleic Acid Atoms 434 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing