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Structure of aminoglycoside phosphotransferase APH(3'')-Id from Streptomyces rimosus ATCC10970 in complex with ADP and streptomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 0.1M MES monohydrate; 12% PEG20000
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.97 α = 90 b = 77.8 β = 90 c = 78.61 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.65 55.3 98.8 0.138 0.151 0.992 8.04 5.952 34969 27.329
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.7 98.2 0.651 0.71 0.825 2.2 6.197
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 6FUC 1.65 55.3 33229 1740 98.8 0.1699 0.1683 0.1826 0.2021 0.2165 RANDOM 28.84
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] -0.52 -2.17 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.543 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 15.265 r_dihedral_angle_1_deg 6.826 r_angle_refined_deg 2.76 r_angle_other_deg 2.519 r_chiral_restr 0.416 r_bond_refined_d 0.021 r_gen_planes_refined 0.016 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.543 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 15.265 r_dihedral_angle_1_deg 6.826 r_angle_refined_deg 2.76 r_angle_other_deg 2.519 r_chiral_restr 0.416 r_bond_refined_d 0.021 r_gen_planes_refined 0.016 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction