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Crystal structure of the S1 domain of RNase E from E. coli (native)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Pb derivative structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 8000, sodium cacodylate, sodium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.378 α = 90 b = 70.378 β = 90 c = 87.917 γ = 90
Symmetry Space Group P 41 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 210 2003-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0781 ALS 8.2.1
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 1.8 50 99 0.05 30.8 7.76 21123 20912 29.2
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) 1.8 1.86 93.5 0.378 4.65
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 SAD THROUGHOUT Pb derivative structure 1.8 50 19874 19874 1012 98.99 0.20009 0.20009 0.19854 0.2063 0.23109 0.2421 RANDOM 27.342
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] 0.82 0.82 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.073 r_scangle_it 4.538 r_scbond_it 2.584 r_mcangle_it 1.948 r_angle_refined_deg 1.315 r_mcbond_it 1.073 r_angle_other_deg 0.736 r_symmetry_vdw_other 0.272 r_nbd_other 0.246 r_symmetry_hbond_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.073 r_scangle_it 4.538 r_scbond_it 2.584 r_mcangle_it 1.948 r_angle_refined_deg 1.315 r_mcbond_it 1.073 r_angle_other_deg 0.736 r_symmetry_vdw_other 0.272 r_nbd_other 0.246 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.085 r_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1327 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing