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Crystal Structure of RlmH in Complex with S-Adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.1 M Tris-bicine buffer (pH 8.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 20% v/v PEG 550 MME, 10% w/v PEG 20,000 in the presence of 2 mM S-Adenosylmethionine
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.53 α = 90 b = 37.36 β = 104.99 c = 122.07 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 100 PIXEL DECTRIS PILATUS 6M-F 2013-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.299 29.5 98.59 0.077 0.999 14.46 5.5 26034
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.47 0.755 0.742 2.18 5.2
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 1NS5 2.299 29.479 1.36 26018 1298 98.53 0.1798 0.1771 0.1872 0.2287 0.2334
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 15.286 f_angle_d 1.318 f_chiral_restr 0.056 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4960 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing