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Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant in complex with RNA obtained by soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.2 M ammonium sulfate, 0.2 M tri-potassium citrate
Crystal Properties Matthews coefficient Solvent content 3.62 65.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.08 α = 90 b = 96.08 β = 90 c = 258.01 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 6M 2019-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.37 51.6 100 0.29 0.293 0.998 12.4 38.2 29657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.41 99.9 2.601 2.633 0.753 1.4 40.2
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 FREE R-VALUE 1URN 2.37 51.031 29570 1498 99.939 0.248 0.2452 0.2444 0.2941 0.2934 43.941
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] 0.775 0.387 0.775 -2.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_4_deg 23.34 r_dihedral_angle_3_deg 16.201 r_lrange_other 7.474 r_lrange_it 7.472 r_dihedral_angle_1_deg 7.059 r_scangle_it 6.029 r_scangle_other 6.029 r_scbond_it 4.259 r_scbond_other 4.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_4_deg 23.34 r_dihedral_angle_3_deg 16.201 r_lrange_other 7.474 r_lrange_it 7.472 r_dihedral_angle_1_deg 7.059 r_scangle_it 6.029 r_scangle_other 6.029 r_scbond_it 4.259 r_scbond_other 4.251 r_mcangle_it 4.135 r_mcangle_other 4.134 r_mcbond_it 2.973 r_mcbond_other 2.972 r_angle_refined_deg 1.592 r_angle_other_deg 1.323 r_nbd_other 0.231 r_symmetry_nbd_other 0.203 r_nbd_refined 0.199 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.115 r_chiral_restr 0.087 r_symmetry_nbd_refined 0.083 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.048 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2269 Nucleic Acid Atoms 1008 Solvent Atoms 26 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing