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Structure of Ribosome maturation protein RimM and Ribosomal protein S19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYI 2DYI AND 2E5L FOR RIMM AND RIBOSOMAL PROTEIN S19, RESPECTIVELY. experimental model PDB 2E5L 2DYI AND 2E5L FOR RIMM AND RIBOSOMAL PROTEIN S19, RESPECTIVELY.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M sodium cacodylate, 0.2M sodium acetate trihydrate, 30%[w/v] polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.397 α = 90 b = 67.491 β = 94.82 c = 62.002 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 95 CCD ADSC QUANTUM 315 2006-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 2.3 50 100 0.108 7.8 3.7 20948 -3
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) 2.3 2.38 100 0.654 2.1 3.8 2079
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DYI AND 2E5L FOR RIMM AND RIBOSOMAL PROTEIN S19, RESPECTIVELY. 2.3 45.57 20934 1076 99.7 0.197 0.191 0.245 0.2392 RANDOM 32.2
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] -0.12 -3.32 2.05 -1.94
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.3 c_scangle_it 3.31 c_mcangle_it 2.7 c_scbond_it 2.16 c_mcbond_it 1.59 c_angle_deg 1.2 c_improper_angle_d 0.81 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3910 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling