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Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.863 α = 90 b = 123.863 β = 90 c = 122.844 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-09 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.99184 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.918370, 0.979440, 0.979035 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 29.748 99.9 0.08 0.08 6.9 8.4 48701
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.3 2.36 98.7 0.602 0.602 1.3 5.5 3384
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 2.3 29.748 48668 2499 99.9 0.161 0.158 0.2575 0.204 0.2752 RANDOM 47.715
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] 1.34 0.67 1.34 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.011 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_1_deg 7.226 r_scangle_it 6.439 r_scbond_it 4.943 r_mcangle_it 2.592 r_mcbond_it 1.749 r_angle_refined_deg 1.572 r_angle_other_deg 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.011 r_dihedral_angle_4_deg 19.92 r_dihedral_angle_3_deg 15.966 r_dihedral_angle_1_deg 7.226 r_scangle_it 6.439 r_scbond_it 4.943 r_mcangle_it 2.592 r_mcbond_it 1.749 r_angle_refined_deg 1.572 r_angle_other_deg 0.985 r_mcbond_other 0.572 r_symmetry_vdw_refined 0.355 r_nbd_refined 0.211 r_nbd_other 0.191 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_other 0.154 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.095 r_nbtor_other 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7174 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction autoSHARP phasing