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Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 298 11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.127 α = 90 b = 234.157 β = 90.65 c = 105.003 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 CCD ADSC QUANTUM 315 2006-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.498 34.94 99.8 0.062 0.046 23.2 6.1 79785 1.1 87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.498 2.59 100 1.1 5.9 7928
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MIR THROUGHOUT 2.498 34.94 2.2 75624 3987 99.35 0.22395 0.22157 0.2548 0.26897 0.279 RANDOM 50.64
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] 0.2 -0.26 -0.02 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_3_deg 16.817 r_dihedral_angle_4_deg 15.145 r_dihedral_angle_1_deg 6.947 r_mcangle_it 1.837 r_angle_refined_deg 1.507 r_scangle_it 1.233 r_mcbond_it 1.201 r_angle_other_deg 0.972 r_scbond_it 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_3_deg 16.817 r_dihedral_angle_4_deg 15.145 r_dihedral_angle_1_deg 6.947 r_mcangle_it 1.837 r_angle_refined_deg 1.507 r_scangle_it 1.233 r_mcbond_it 1.201 r_angle_other_deg 0.972 r_scbond_it 0.816 r_mcbond_other 0.326 r_symmetry_hbond_refined 0.242 r_nbtor_refined 0.224 r_nbd_other 0.219 r_xyhbond_nbd_refined 0.196 r_symmetry_vdw_other 0.189 r_nbd_refined 0.154 r_symmetry_vdw_refined 0.144 r_metal_ion_refined 0.12 r_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2908 Nucleic Acid Atoms 13080 Solvent Atoms 206 Heterogen Atoms 80
Software Software Software Name Purpose CBASS data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling