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Crystal structure of the SpoU Methyltransferase AviRb from Streptomyces viridochromogenes in complex with the cofactor AdoMet
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 PEG 300, MES, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.881 α = 90 b = 76.881 β = 90 c = 209.818 γ = 90
Symmetry Space Group P 41 21 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 MARRESEARCH 2003-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9762 SLS X06SA
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 2.55 25 100 0.064 0.076 18.8 9.4 21375 2 2 55.6
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 2.55 2.68 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.55 25 20283 20283 1067 100 0.20477 0.202 0.2058 0.25653 0.2514 RANDOM 25.26
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] -0.12 -0.12 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.866 r_scangle_it 2.312 r_angle_refined_deg 1.426 r_scbond_it 1.315 r_angle_other_deg 0.86 r_mcangle_it 0.857 r_mcbond_it 0.452 r_symmetry_vdw_other 0.231 r_nbd_other 0.22 r_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.866 r_scangle_it 2.312 r_angle_refined_deg 1.426 r_scbond_it 1.315 r_angle_other_deg 0.86 r_mcangle_it 0.857 r_mcbond_it 0.452 r_symmetry_vdw_other 0.231 r_nbd_other 0.22 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.135 r_nbtor_other 0.085 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3955 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing