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Crystal structure of the SpoU Methyltransferase AviRb from Streptomyces viridochromogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 PEG 200, MES, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.623 α = 90 b = 76.623 β = 90 c = 208.935 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 2004-04-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9793,0.9790,0.9611 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 2.37 25 99.6 0.048 0.051 23.5 6.5 26199 2 2 58
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 2.37 2.41 99.9 0.248 0.347 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MAD THROUGHOUT 2.37 25 2 24896 24851 1262 99.82 0.20766 0.20561 0.2272 0.24899 0.2593 RANDOM 32.922
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 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.687 r_scangle_it 2.447 r_scbond_it 1.481 r_angle_refined_deg 1.325 r_mcangle_it 0.986 r_angle_other_deg 0.856 r_mcbond_it 0.527 r_symmetry_vdw_other 0.252 r_nbd_other 0.225 r_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.687 r_scangle_it 2.447 r_scbond_it 1.481 r_angle_refined_deg 1.325 r_mcangle_it 0.986 r_angle_other_deg 0.856 r_mcbond_it 0.527 r_symmetry_vdw_other 0.252 r_nbd_other 0.225 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.196 r_nbtor_other 0.084 r_chiral_restr 0.078 r_symmetry_vdw_refined 0.052 r_bond_refined_d 0.013 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3998 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHARP phasing