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Crystal structure of the RC3H2 ROQ domain in complex with stem-loop and double-stranded forms of RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 The protein was diluted to 6.7 mg/ml then mixed with IER3 RNA at a ratio
1:2 before crystallized. 17% PEG10000, 0.1 M Bis-Tris pH6.5, 5% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.25 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.299 α = 90 b = 174.734 β = 114.12 c = 61.29 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2014-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 99.1 0.083 0.09 0.036 8.4 5.9 39757 50.3
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 2.5 2.54 97.6 0.83 0.913 0.377 0.801 5.4 1955
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 4QIK 2.5 50 38676 822 98.91 0.2454 0.2451 0.246 0.2592 0.2504 RANDOM 62.219
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] -0.1 0.54 -0.84 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.01 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 13.394 r_dihedral_angle_1_deg 4.693 r_mcangle_it 3.275 r_mcbond_it 2.017 r_mcbond_other 2.017 r_angle_other_deg 1.218 r_angle_refined_deg 1.094 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.01 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 13.394 r_dihedral_angle_1_deg 4.693 r_mcangle_it 3.275 r_mcbond_it 2.017 r_mcbond_other 2.017 r_angle_other_deg 1.218 r_angle_refined_deg 1.094 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4534 Nucleic Acid Atoms 1221 Solvent Atoms 40 Heterogen Atoms 3
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing