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Crystal structure of Era in complex with MgGDPNP, nucleotides 1506-1542 of 16S ribosomal RNA, and KsgA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IEV 3IEV, 3FTF experimental model PDB 3FTF 3IEV, 3FTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292 0.1M sodium acetate, 20% (v/v) MPD, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.502 α = 90 b = 68.094 β = 100.62 c = 73.587 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD mirrors 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 2.8 30 98.4 0.097 9.4 4.8 23217 23217 -6 -3 56.8
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 2.8 2.9 91 0.614 1.69 3.2 2114
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3IEV, 3FTF 2.8 28.686 0.09 22561 22561 975 95.44 0.1735 0.171 0.1709 0.2255 0.2241 random 75.835
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] 4.9656 -7.4092 -8.1605 -0.7229
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.35 f_angle_d 1.24 f_chiral_restr 0.074 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4284 Nucleic Acid Atoms 744 Solvent Atoms 83 Heterogen Atoms 57
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction