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Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.05M MES, 15mM MgS04, 7% PEG 4000, 20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 57.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.377 α = 90 b = 91.86 β = 90 c = 96.931 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 ADSC QUANTUM 315 2007-11-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.00931 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 30 97 0.078 0.078 21.2 6.3 17064 16553
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) 2.9 3 76.5 0.361 2.9 1265
Refinement Statistics Diffraction ID Structure Solution 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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2V3J 3 29.886 1.36 15321 15321 761 99.17 0.1901 0.1901 0.1864 0.1728 0.2597 0.2444 70.9897
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] -1.487 1.0985 0.3885
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.517 f_angle_d 1.29 f_chiral_restr 0.078 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3364 Nucleic Acid Atoms 586 Solvent Atoms 61 Heterogen Atoms 51
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction HKL-2000 data scaling MOLREP phasing