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Crystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 483D PDB entry 483D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 ammonium sulfate, K-MOPS, magnesium chloride, spermine, cobalt chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.143 α = 90 b = 42.143 β = 90 c = 336.167 γ = 90
Symmetry Space Group P 43 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 4 2000-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
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 2.25 40 99.6 0.077 41.1 9.5 15628 15569
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) 2.25 2.29 98 0.473 6.8
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 483D 2.25 40 15628 15161 1511 97 0.227 0.227 0.225 0.2234 0.266 0.264 Random
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 c_scangle_it 1.845 c_mcangle_it 1.646 c_scbond_it 1.377 c_mcbond_it 1.121 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 1.845 c_mcangle_it 1.646 c_scbond_it 1.377 c_mcbond_it 1.121 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1734 Solvent Atoms 99 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling EPMR phasing CNS refinement HKL-2000 data reduction