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Crystal structure of a Ribosomal RNA small subunit methyltransferase E from Neisseria gonorrhoeae bound to S-adenosyl methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 NegoA.00176.a.B1.PW37905 at 20 mg/mL with 4 mM SAM against JCSG+ screen condition C4 10% PEG 6000, 0.1 M Hepes pH 7.0 supplemented with 20% EG and 2.5 mM AMP as cryo-protectant, crystal tracking ID 273658c4. unique puck ID llm2-5
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.3 α = 90 b = 71.54 β = 90 c = 120.65 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 100 CCD MARMOSAIC 300 mm CCD 2016-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.4 28.944 98.3 0.046 0.051 0.999 21.2 4.906 21718 -3 51.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 99.4 0.552 0.614 0.857 2.69 4.744
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1nxz 2.4 28.944 1.35 21682 1902 98.26 0.2006 0.1954 0.2099 0.2536 0.2604 66.3046
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 f_dihedral_angle_d 16.522 f_angle_d 1.015 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3471 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 27
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing