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Structure of a S-adenosylmethionine synthetase from Mycobacterium avium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RG9 PDB entry 1RG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 14.4% PEG8000, 20% glycerol, 80mM cacodylate pH 6.5, 160mM Calcium acetate. protein 11.42 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.03 α = 90 b = 88.18 β = 90 c = 184.19 γ = 90
Symmetry Space Group P 2 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 210 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97 ALS 5.0.1
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 1.73 185 97.2 0.042 21.03 100009 -3 22.778
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 1.73 1.77 80.7 0.248 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 1RG9 1.73 20 99729 4970 96.95 0.1576 0.1566 0.1645 0.1774 0.1833 RANDOM 16.4196
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] -0.08 1.18 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.694 r_dihedral_angle_4_deg 12.909 r_dihedral_angle_3_deg 10.962 r_dihedral_angle_1_deg 5.669 r_scangle_it 3.549 r_scbond_it 2.041 r_angle_refined_deg 1.309 r_mcangle_it 1.236 r_angle_other_deg 0.894 r_mcbond_it 0.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.694 r_dihedral_angle_4_deg 12.909 r_dihedral_angle_3_deg 10.962 r_dihedral_angle_1_deg 5.669 r_scangle_it 3.549 r_scbond_it 2.041 r_angle_refined_deg 1.309 r_mcangle_it 1.236 r_angle_other_deg 0.894 r_mcbond_it 0.666 r_mcbond_other 0.173 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5651 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction