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Structure of aminoglycoside phosphotransferase APH(3'')-Id from Streptomyces rimosus ATCC10970
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277 0.1M Tacsimate; 17% PEG3350; 10% sucrose.
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.37 α = 90 b = 77.66 β = 90 c = 78.59 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 2015-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.17 55.24 99.4 0.185 0.207 0.091 0.966 5.7 4.8 98425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.19 99.4 0.391 0.437 0.19 0.869 5
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 4GKH 1.17 55.24 93604 4751 99.23 0.1394 0.1378 0.1434 0.1687 0.1711 RANDOM 16.001
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] 0.84 -0.57 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.751 r_sphericity_free 28.82 r_dihedral_angle_4_deg 20.708 r_sphericity_bonded 15.05 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_1_deg 5.954 r_rigid_bond_restr 3.41 r_angle_refined_deg 2.129 r_angle_other_deg 1.085 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.751 r_sphericity_free 28.82 r_dihedral_angle_4_deg 20.708 r_sphericity_bonded 15.05 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_1_deg 5.954 r_rigid_bond_restr 3.41 r_angle_refined_deg 2.129 r_angle_other_deg 1.085 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction