☰ Navigation Tabs
Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Preliminary assigned NMR model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 25mM Tris-HCl, 0.025% w/v Polyethylene glycol 6000, 0.5M Lithium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.328 α = 90 b = 53.103 β = 90 c = 70.437 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 210 mirrors 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 42.4 100 0.083 23.8 7.17 13576 -3 6.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.314 6.93 7.3 1316
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 Preliminary assigned NMR model 2 42.4 13529 654 99.9 0.192 0.192 0.1918 0.256 0.2562 RANDOM 23.3
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] -3.28 4.27 -0.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.6 c_scangle_it 5.03 c_scbond_it 3.45 c_mcangle_it 2.77 c_mcbond_it 2.09 c_angle_deg 2 c_improper_angle_d 1.28 c_bond_d 0.022 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.6 c_scangle_it 5.03 c_scbond_it 3.45 c_mcangle_it 2.77 c_mcbond_it 2.09 c_angle_deg 2 c_improper_angle_d 1.28 c_bond_d 0.022 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1280 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction HKL-2000 data scaling PHASER phasing