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Group I self-splicing intron P4-P6 domain mutant U131A (with isopropanol soaking)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 PEG 1000, sodium cacodylate, spermine
Crystal Properties Matthews coefficient Solvent content 3.48 64.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.67 α = 90 b = 130.01 β = 90 c = 146.41 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 2016-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979100 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.14 63.8 98.9 16.3 12.9 25244 113.088043928
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 1GID 3.14 63.8 1.32948920372 25212 2520 98.7466708444 0.213003674255 0.211184378342 0.2163 0.22924417573 0.2317 128.619241904
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 15.0161921613 f_angle_d 0.633355654452 f_chiral_restr 0.0416861274456 f_plane_restr 0.00398600576193 f_bond_d 0.00300655661399
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 6770 Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement BUSTER refinement XDS data reduction XSCALE data scaling PHENIX phasing