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Crystal Structure of RNase L in complex with 2-5A and AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G8K PDB ENTRY 4G8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 5 mM MgCl2, 5 mM DTT, 18% PEG2000, 100 mM NaCl, and 100 mM SPG buffer, pH 7. , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.197 α = 90 b = 267.392 β = 90.04 c = 110.21 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 PIXEL DECTRIS PILATUS 6M 2013-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 59.2 95.7 0.104 6.8 3 106347 1.6 1.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.504 2.569 88.4 0.526 1.6 3.2 7277
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MR-SAD THROUGHOUT PDB ENTRY 4G8K 2.5 59.2 1.6 111125 106347 5725 95.67 0.1975 0.19568 0.1966 0.23107 0.2315 RANDOM 51.977
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] 2.95 1.86 -18.36 15.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 18.386 r_dihedral_angle_3_deg 16.195 r_long_range_B_refined 9.069 r_long_range_B_other 9.065 r_dihedral_angle_1_deg 5.394 r_scangle_other 4.616 r_mcangle_it 4.357 r_mcangle_other 4.357 r_scbond_it 2.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 18.386 r_dihedral_angle_3_deg 16.195 r_long_range_B_refined 9.069 r_long_range_B_other 9.065 r_dihedral_angle_1_deg 5.394 r_scangle_other 4.616 r_mcangle_it 4.357 r_mcangle_other 4.357 r_scbond_it 2.789 r_scbond_other 2.788 r_mcbond_it 2.695 r_mcbond_other 2.692 r_angle_refined_deg 1.231 r_angle_other_deg 0.832 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21367 Nucleic Acid Atoms Solvent Atoms 1030 Heterogen Atoms 432
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling