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Crystal structure of a putative s-adenosyl-l-methionine-dependent methyltransferase (mmp1179) from methanococcus maripaludis at 1.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.17M ammonium acetate, 15.0% Glycerol, 25.5% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, Additive - 1mM S-adenosylmethionine, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.61 α = 90 b = 63.5 β = 90 c = 75.44 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 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-06-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97947 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 1.15 29.26 98 0.037 11.43 68022 -3 7.892
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 1.15 1.19 94.2 0.378 2.3
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 1.15 29.26 67971 3439 99.46 0.121 0.12 0.12 0.138 0.1373 RANDOM 9.085
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] 0.62 0.16 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_4_deg 17.48 r_dihedral_angle_3_deg 11.665 r_sphericity_free 7.559 r_scangle_it 5.12 r_dihedral_angle_1_deg 4.988 r_scbond_it 3.919 r_sphericity_bonded 3.369 r_mcangle_it 2.575 r_rigid_bond_restr 2.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_4_deg 17.48 r_dihedral_angle_3_deg 11.665 r_sphericity_free 7.559 r_scangle_it 5.12 r_dihedral_angle_1_deg 4.988 r_scbond_it 3.919 r_sphericity_bonded 3.369 r_mcangle_it 2.575 r_rigid_bond_restr 2.217 r_mcbond_it 1.776 r_angle_refined_deg 1.723 r_angle_other_deg 1.342 r_mcbond_other 0.856 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing