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xpt-pbuX C74U Riboswitch from B. subtilis bound to 24-diamino-1,3,5- triazine identified by virtual screening
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G9C PDB ENTRY 2G9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10MM K-HEPES PH 7.5, 25% PEG 3000, 12MM COHEX, 800MM AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.923 α = 90 b = 34.94 β = 90.11 c = 42.074 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 100 CCD ADSC CCD 2009-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.7 65.51 96.8 0.05 26.8 3 21077
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 1.7 1.76 93.5 0.39 3.1
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 2G9C 1.7 65.46 19531 1054 96.8 0.21891 0.21605 0.2134 0.27082 0.2673 RANDOM 29.103
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] 2.07 -0.44 -1.74 -0.33
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.47 r_angle_refined_deg 1.973 r_scbond_it 1.796 r_mcangle_it 0.36 r_mcbond_it 0.249 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.47 r_angle_refined_deg 1.973 r_scbond_it 1.796 r_mcangle_it 0.36 r_mcbond_it 0.249 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1363 Solvent Atoms 151 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing