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In vitro evolved glmS ribozyme triple mutant, calcium ion complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z75 PDB entry 2Z75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 10% PEG 8000, 1 M lithium chloride, 50mM magnesium acetate, 50mM calcium chloride, 1mM spermine, 50mM cacodylate, 50mM HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.8 56.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.91 α = 90 b = 41.17 β = 90 c = 75.85 γ = 90
Symmetry Space Group P 21 21 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 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 3.1 30 96.9 0.027 23.6 4.1 9873 3.2
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 3.1 3.15 96.1 1.123 3.2 4.1 476
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Z75 3.12 28.86 9861 9861 747 93.6 0.231 0.231 0.231 0.2269 0.273 0.2683 RANDOM 106
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] 1.26 -20.43 19.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 14.1 c_improper_angle_d 1.36 c_angle_deg 0.9 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 14.1 c_improper_angle_d 1.36 c_angle_deg 0.9 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2996 Solvent Atoms 2 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling