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Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.68 α = 90 b = 55.94 β = 102.9 c = 61.22 γ = 90
Symmetry Space Group C 1 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 collimating mirror, toroid focusing mirror 2008-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915 SSRL BL9-2
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 29.735 98.2 0.055 10.33 20496 -3 29.356
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 96.5 0.322 2.4
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 SAD THROUGHOUT 2.15 29.735 20494 1050 99.64 0.171 0.168 0.1724 0.228 0.2324 RANDOM 26.368
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] -0.56 -0.19 1.11 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_3_deg 13.222 r_scangle_it 6.405 r_dihedral_angle_1_deg 5.588 r_scbond_it 4.455 r_mcangle_it 2.425 r_mcbond_it 1.35 r_angle_refined_deg 1.174 r_angle_other_deg 0.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_3_deg 13.222 r_scangle_it 6.405 r_dihedral_angle_1_deg 5.588 r_scbond_it 4.455 r_mcangle_it 2.425 r_mcbond_it 1.35 r_angle_refined_deg 1.174 r_angle_other_deg 0.906 r_mcbond_other 0.321 r_symmetry_vdw_other 0.258 r_nbd_refined 0.206 r_nbd_other 0.196 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.152 r_nbtor_other 0.084 r_chiral_restr 0.07 r_metal_ion_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2531 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 52
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