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Crystal structure of DEAH-box ATPase Prp22-S837A with bound ssRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Bis-Tris propane pH 8.5, 250 mM NaF, 22% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.61 α = 90 b = 139.96 β = 90 c = 164.66 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 EIGER X 16M 2018-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97620 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.7 106.49 99.7 0.077 0.081 1 19.56 9.251 88822 81.23
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 2.7 2.82 99.8 1.474 1.561 0.705 1.69 9.442
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6I3P 2.7 106.49 84380 4441 99.72 0.2146 0.2122 0.2134 0.2614 0.2578 RANDOM 85.903
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] -3.37 -1.94 5.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.135 r_dihedral_angle_4_deg 18.332 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_1_deg 5.804 r_angle_other_deg 2.295 r_angle_refined_deg 1.511 r_chiral_restr 0.079 r_bond_other_d 0.034 r_gen_planes_other 0.011 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.135 r_dihedral_angle_4_deg 18.332 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_1_deg 5.804 r_angle_other_deg 2.295 r_angle_refined_deg 1.511 r_chiral_restr 0.079 r_bond_other_d 0.034 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19755 Nucleic Acid Atoms 832 Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing Coot model building