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Crystal structure of the cobalamin riboswitch aptamer domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 298 100 mM magnesium acetate, 10% 2-methyl-1,3-propanediol, 5 mM iridium hexammine, pH 7.0, hanging drop, temperature 298K 2 hanging drop 7 298 100 mM magnesium acetate, 10% 2-methyl-1,3-propanediol, 5 mM iridium hexammine, pH 7.0, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.7 66.5 3.7 66.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.03 α = 90 b = 142.03 β = 90 c = 137.9 γ = 120
Symmetry Space Group P 64 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 CCD ADSC QUANTUM 315 2010-12-12 M MAD 2 2
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.1051, 1.6 ALS 5.0.2 2 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.95 137.899 99.9 0.098 20.6 13.7 17854 17854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.11 100 0.014 1.406 0.5 14.2 2536
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.95 43.06 18377 17822 910 99.92 0.2397 0.2397 0.2393 0.2494 0.2491 0.2529 RANDOM 103.2693
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]
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.89 t_angle_deg 0.64 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.89 t_angle_deg 0.64 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact t_omega_torsion
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3600 Solvent Atoms Heterogen Atoms 217
Software Software Software Name Purpose SCALA data scaling SHARP phasing SOLOMON phasing BUSTER-TNT refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction BUSTER refinement