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Crystal structure of S-Adenosylmethionine synthase from Sulfolobus solfataricus complexed with SAM and PPi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 Protein Solution (6.8-13.5 mg/ml protein in 25mM Tris pH 8.0, 5mM SAM) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6). Cryoprotected with 25% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.14 70.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.597 α = 90 b = 151.597 β = 90 c = 226.125 γ = 120
Symmetry Space Group P 65 2 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 MARMOSAIC 300 mm CCD 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.19 50 100 0.142 6.7 19.5 79075 79075
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.23 100 14.3 3885
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 (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 4HPV 2.189 49.622 1.35 79075 78976 3960 99.73 0.1651 0.1639 0.1699 0.1888 0.1944 ASSIGN TEST SET IN THIN RESOLUTION SHELLS 32.7212
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 12.492 f_angle_d 1.022 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6232 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHENIX phasing