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Crystal structure of the alpha subunit of human S-adenosylmethionine synthetase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QM4 PDB entry 1QM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.2M Lithium chloride, 0.1M Tris-HCl, 20% PEG 6000, 10.0% Ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.301 α = 90 b = 94.106 β = 90 c = 117.383 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 CCD MARMOSAIC 225 mm CCD 2006-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97600 SLS X10SA
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 1.21 73.52 99 0.0501 23.09 7.16 113895 113895
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) 1.21 1.3 97.5 0.1849 10.93 6.48
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1QM4 1.21 73.52 108185 108185 5709 99.01 0.1008 0.1008 0.09981 0.1002 0.11946 0.1194 RANDOM 7.3
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] 0.75 -0.57 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_4_deg 21.319 r_dihedral_angle_3_deg 11.051 r_sphericity_free 7.745 r_dihedral_angle_1_deg 6.622 r_scangle_it 3.736 r_sphericity_bonded 3.117 r_scbond_it 2.894 r_mcangle_it 1.944 r_angle_refined_deg 1.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_4_deg 21.319 r_dihedral_angle_3_deg 11.051 r_sphericity_free 7.745 r_dihedral_angle_1_deg 6.622 r_scangle_it 3.736 r_sphericity_bonded 3.117 r_scbond_it 2.894 r_mcangle_it 1.944 r_angle_refined_deg 1.615 r_mcbond_it 1.576 r_rigid_bond_restr 1.258 r_angle_other_deg 0.993 r_mcbond_other 0.546 r_symmetry_vdw_other 0.261 r_nbd_refined 0.228 r_nbd_other 0.203 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.103 r_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3030 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing