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Crystal structure of DEAH-box ATPase Prp22 with bound ssRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100mM Bis-Tris propane pH8.5, 250mM NaF, 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.79 α = 90 b = 140.5 β = 90 c = 159.55 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 2018-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9919 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.75 49.24 99.9 0.11 0.118 0.999 14.28 7.791 82130 72.839
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 2.75 2.87 100 1.469 1.567 0.75 1.51 8.154
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 6fa5 2.75 49.24 78023 4107 99.93 0.2233 0.2218 0.2242 0.2531 0.2548 RANDOM 72.077
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] -2.08 -0.43 2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.536 r_dihedral_angle_4_deg 15.936 r_dihedral_angle_3_deg 13.345 r_dihedral_angle_1_deg 4.845 r_angle_other_deg 2.283 r_angle_refined_deg 1.772 r_chiral_restr 0.112 r_bond_other_d 0.034 r_gen_planes_other 0.017 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.536 r_dihedral_angle_4_deg 15.936 r_dihedral_angle_3_deg 13.345 r_dihedral_angle_1_deg 4.845 r_angle_other_deg 2.283 r_angle_refined_deg 1.772 r_chiral_restr 0.112 r_bond_other_d 0.034 r_gen_planes_other 0.017 r_bond_refined_d 0.015 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19804 Nucleic Acid Atoms 736 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction