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Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 3.6M sodium formate, 10.0% Glycerol, Additive 0.001 M S-adenosylmethionine (SAM), VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 5.3 76.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.433 α = 90 b = 130.433 β = 90 c = 54.431 γ = 120
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 325 mm CCD Flat mirror (vertical focusing) 2008-08-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97920,0.97845 SSRL BL11-1
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 2.1 28.239 99.9 0.068 8.039 5.6 31089 38.343
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 2.1 2.15 100 0.521 1.5 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 28.239 31072 1568 99.88 0.159 0.158 0.1614 0.176 0.1769 RANDOM 46.049
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] -1.63 -0.82 -1.63 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.91 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 10.759 r_scangle_it 7.107 r_scbond_it 5.234 r_dihedral_angle_1_deg 3.779 r_mcangle_it 3.079 r_mcbond_it 2.364 r_angle_refined_deg 1.637 r_angle_other_deg 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.91 r_dihedral_angle_4_deg 18.651 r_dihedral_angle_3_deg 10.759 r_scangle_it 7.107 r_scbond_it 5.234 r_dihedral_angle_1_deg 3.779 r_mcangle_it 3.079 r_mcbond_it 2.364 r_angle_refined_deg 1.637 r_angle_other_deg 1 r_mcbond_other 0.55 r_symmetry_vdw_other 0.323 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.218 r_nbd_other 0.202 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.099 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1699 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction autoSHARP phasing SHELXD phasing