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Crystal structure of SMU.776, a putative methyltransferase complexed with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B78 PDB ENTRY 2B78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 8000, 0.1M Na cacodylate pH6.5, 0.2M MgAc2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.684 α = 90 b = 50.828 β = 107.14 c = 59.569 γ = 90
Symmetry Space Group C 1 2 1
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 BRUKER SMART 6000 2005-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 56.18 90.75 0.0399 10.73 2.25 24306 22057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.33 71.9
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 2B78 2.23 12 20503 1113 93.18 0.17649 0.17347 0.1905 0.23199 0.2533 RANDOM 27.061
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] -0.11 -0.14 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.074 r_dihedral_angle_4_deg 20.032 r_dihedral_angle_3_deg 16.587 r_dihedral_angle_1_deg 7.077 r_scangle_it 4.101 r_scbond_it 2.712 r_angle_refined_deg 1.778 r_mcangle_it 1.583 r_mcbond_it 0.927 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.074 r_dihedral_angle_4_deg 20.032 r_dihedral_angle_3_deg 16.587 r_dihedral_angle_1_deg 7.077 r_scangle_it 4.101 r_scbond_it 2.712 r_angle_refined_deg 1.778 r_mcangle_it 1.583 r_mcbond_it 0.927 r_chiral_restr 0.133 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3048 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 26
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling