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Structural insights of MAT enzymes: MATa2b complexed with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PO2 PDB ENTRIES 2PO2 AND 2YDY experimental model PDB 2YDY PDB ENTRIES 2PO2 AND 2YDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 0.1M MES/Imidazole pH 6.5
0.1M Carboxylic acids
20% Ethylene glycol
10% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.442 α = 90 b = 115.723 β = 90 c = 298.455 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 PIXEL PSI PILATUS 6M 2013-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 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 2.59 50 98.7 0.144 5.6 78380 77361 1.75 1.75
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 2.6 2.69 90.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRIES 2PO2 AND 2YDY 2.59 47.41 78380 76590 3847 96.8 0.221 0.218 0.2167 0.279 0.2756 75.2
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] 3.29 -0.06 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 13.337 r_dihedral_angle_1_deg 5.884 r_angle_refined_deg 1.091 r_angle_other_deg 0.71 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 13.337 r_dihedral_angle_1_deg 5.884 r_angle_refined_deg 1.091 r_angle_other_deg 0.71 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16216 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement