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Crystal Structure of Human methyltransferase AD-003 in complex with S-adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 300 Purified AD-003 was was complexed with S-adenosyl-L-homocysteine (SAH) (Sigma) at 1:5 molar ratio of protein:SAH and crystallized using the hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 18% PEG 3350, 0.2 M KCl, 0.1 M glycine, pH 9.5., VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.922 α = 105.72 b = 47.367 β = 88.18 c = 64.734 γ = 115.97
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 MARRESEARCH 2005-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 100 92.2 41514 41514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.79 92.3
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 1XTP 1.75 62.02 39433 39433 2071 91.85 0.19731 0.19731 0.19398 0.1974 0.25789 0.2001 RANDOM 23.848
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] -0.8 -0.12 -0.03 0.38 0.1 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.778 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 5.774 r_scangle_it 2.985 r_scbond_it 1.988 r_angle_refined_deg 1.345 r_mcangle_it 1.306 r_mcbond_it 0.839 r_symmetry_vdw_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.778 r_dihedral_angle_4_deg 16.363 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 5.774 r_scangle_it 2.985 r_scbond_it 1.988 r_angle_refined_deg 1.345 r_mcangle_it 1.306 r_mcbond_it 0.839 r_symmetry_vdw_refined 0.306 r_nbtor_refined 0.303 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3528 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing