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The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGK PDB entry 1VGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 10% w/v PEG8000, 200 mM magnesium acetate
Crystal Properties Matthews coefficient Solvent content 2.4348 49.5142
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.37 α = 90 b = 66.2 β = 92.42 c = 56.79 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2020-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-E 0.98 APS 21-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 41.349 90.4 0.069 0.096 0.067 0.993 14.6 2.3 23784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 97 0.281 0.396 0.278 0.899 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1VGK 2.066 41.349 23784 1254 90.245 0.204 0.2027 0.2099 0.2335 0.2296 46.908
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] -0.426 0.163 3.235 -2.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.388 r_dihedral_angle_3_deg 16.067 r_lrange_it 8.08 r_dihedral_angle_1_deg 7.677 r_scangle_it 5.805 r_dihedral_angle_2_deg 5.714 r_scbond_it 4.248 r_mcangle_it 4.188 r_mcbond_it 3.064 r_angle_refined_deg 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.388 r_dihedral_angle_3_deg 16.067 r_lrange_it 8.08 r_dihedral_angle_1_deg 7.677 r_scangle_it 5.805 r_dihedral_angle_2_deg 5.714 r_scbond_it 4.248 r_mcangle_it 4.188 r_mcbond_it 3.064 r_angle_refined_deg 1.874 r_symmetry_nbd_refined 0.501 r_symmetry_xyhbond_nbd_refined 0.326 r_nbtor_refined 0.316 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.12 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement BUCCANEER model building SCALEPACK data scaling PHASER phasing