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Xanthin riboswitch in complex with oxypurinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ELP 7ELP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 287 0.1M ammonium sulfate, 0.1M sodium chloride, 20% PEG 8000, 1M sodium formate, 50mM Bis-Tris
Crystal Properties Matthews coefficient Solvent content 5.05 75.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.811 α = 90 b = 85.091 β = 90 c = 97.162 γ = 90
Symmetry Space Group I 2 2 2
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 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.102 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.63 50 98 0.1 0.013 1 4.2 12 6639 97
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 2.66 2.76 84.9 1.047 2.9 0.2 9.6
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 7ELP 2.63 21.34 6620 318 71.5 0.2391 0.2371 0.2381 0.2819 0.2729 RANDOM 123.43
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] 7.4481 0.3076 -7.7557
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.06 t_angle_deg 0.78 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 987 Solvent Atoms 17 Heterogen Atoms 11
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing