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The structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9S PDB ENTRY 1C9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00
Crystal Properties Matthews coefficient Solvent content 4.4 72.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.907 α = 90 b = 133.986 β = 100.11 c = 232.826 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 35 92.2 0.056 19.3 3.3 251906
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 1.9 1.97 58 0.284 2.7 2.2
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 PDB ENTRY 1C9S 1.9 20 249451 1248 100 0.186 0.186 0.2295 0.236 0.2581 RANDOM 13.53
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] 2.93 2.02 -1.32 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.164 r_scangle_it 6.588 r_scbond_it 5.166 r_mcangle_it 2.148 r_angle_refined_deg 1.422 r_mcbond_it 1.206 r_symmetry_vdw_refined 0.242 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.164 r_scangle_it 6.588 r_scbond_it 5.166 r_mcangle_it 2.148 r_angle_refined_deg 1.422 r_mcbond_it 1.206 r_symmetry_vdw_refined 0.242 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11960 Nucleic Acid Atoms 584 Solvent Atoms 1682 Heterogen Atoms 330
Software Software Software Name Purpose AMoRE model building REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing