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Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with the product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QM4 PDB entries 1QM4,2HJ2 experimental model PDB 2HJ2 PDB entries 1QM4,2HJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 200 mM NaF, 20 % PEG 3350, 10 % ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.404 α = 90 b = 95.016 β = 90 c = 115.773 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE RIGAKU RAXIS HTC OSMIC 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
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 2.05 50 93.5 0.09 0.069 9.7 5.2 22880 21754 2 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 93.5 0.284 0.263 5.1 3.4 2102
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 1QM4,2HJ2 2.05 50 21754 21754 1125 98.86 0.1411 0.1411 0.13895 0.18315 0.1894 RANDOM 18.06
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] 0.89 -0.95 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 6.398 r_scangle_it 2.864 r_scbond_it 1.768 r_angle_refined_deg 1.383 r_mcangle_it 0.986 r_angle_other_deg 0.957 r_mcbond_it 0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 6.398 r_scangle_it 2.864 r_scbond_it 1.768 r_angle_refined_deg 1.383 r_mcangle_it 0.986 r_angle_other_deg 0.957 r_mcbond_it 0.524 r_symmetry_vdw_other 0.244 r_symmetry_vdw_refined 0.202 r_nbd_other 0.197 r_nbd_refined 0.189 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.152 r_mcbond_other 0.143 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing