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Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa Kanamycin A Complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 50 mM HEPES, 17% PEG4000, 10% glycerol, 5% isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.903 α = 90 b = 101.426 β = 100.61 c = 73.399 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ VariMax HF 2011-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.09 50 99.7 0.32 7 32419 32322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 98.9 0.32 4.6 5.8 3356
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 2.15 50 31904 31811 1685 99.71 0.19829 0.19829 0.19537 0.1954 0.25052 0.2525 RANDOM 30.421
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] 2.25 -0.03 -2 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 6.35 r_scangle_it 4.781 r_scbond_it 3.134 r_mcangle_it 1.88 r_angle_refined_deg 1.871 r_mcbond_it 1.06 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 20.163 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 6.35 r_scangle_it 4.781 r_scbond_it 3.134 r_mcangle_it 1.88 r_angle_refined_deg 1.871 r_mcbond_it 1.06 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4832 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 67
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling