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The crystal structure of an RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other a different crystal form of same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 25% PEG3350, 0.2 M amonium sulfate, 0.1 M bis-tris, pH 6.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.9 35.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.728 α = 90 b = 39.748 β = 103.56 c = 56.238 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 IMAGE PLATE RIGAKU RAXIS 2014-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 34.73 97.1 0.112 8.5 3.6 14029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 90.7 0.587 0.369 2.3 3.3 773
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 a different crystal form of same protein 1.8 30 14013 700 97.17 0.2064 0.2034 0.2124 0.2636 0.2676 RANDOM 21.3503
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] -1.33 0.74 -1.57 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.952 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 11.705 r_dihedral_angle_1_deg 6.206 r_mcangle_it 2.749 r_mcbond_it 1.826 r_mcbond_other 1.825 r_angle_refined_deg 1.371 r_angle_other_deg 0.792 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.952 r_dihedral_angle_4_deg 15.135 r_dihedral_angle_3_deg 11.705 r_dihedral_angle_1_deg 6.206 r_mcangle_it 2.749 r_mcbond_it 1.826 r_mcbond_other 1.825 r_angle_refined_deg 1.371 r_angle_other_deg 0.792 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1275 Nucleic Acid Atoms 106 Solvent Atoms 89 Heterogen Atoms 7
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction