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Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 NANODROP, 0.214M Ammonium nitrate, 14.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.66 α = 90 b = 119.17 β = 90 c = 122.58 γ = 90
Symmetry Space Group I 2 2 2
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) 2007-04-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97926, 0.97891 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 2.15 29.788 96.1 0.097 7.69 3.24 29426 -3 24.43
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 2.15 2.23 94.6 0.424 2.2
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 (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 MAD THROUGHOUT 2.15 29.788 29425 1494 98.94 0.169 0.169 0.166 0.1751 0.224 0.2288 RANDOM 28.849
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] 0.07 0.63 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.33 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_3_deg 11.007 r_scangle_it 6.114 r_scbond_it 4.971 r_dihedral_angle_1_deg 4.065 r_mcangle_it 2.946 r_mcbond_it 2.13 r_angle_refined_deg 1.747 r_angle_other_deg 1.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.33 r_dihedral_angle_4_deg 16.555 r_dihedral_angle_3_deg 11.007 r_scangle_it 6.114 r_scbond_it 4.971 r_dihedral_angle_1_deg 4.065 r_mcangle_it 2.946 r_mcbond_it 2.13 r_angle_refined_deg 1.747 r_angle_other_deg 1.065 r_mcbond_other 0.523 r_symmetry_vdw_other 0.265 r_xyhbond_nbd_refined 0.227 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.194 r_nbtor_refined 0.179 r_nbd_other 0.174 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.115 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2956 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing