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Crystal structure of aminoglycoside acetyltransferase AAC(6')-Ib in complex whith coenzyme A and kanamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRB pdb entry 2prb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 K2HPO4 1.5 M, NaH2PO4 0.06M, Guanidine 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.404 α = 90 b = 57.404 β = 90 c = 145.57 γ = 90
Symmetry Space Group P 43 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 77 CCD ADSC QUANTUM 210 2007-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.4 53.402 100 0.081 0.081 8.3 13.4 10187 10187 3
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 2.4 2.53 100 0.212 0.212 3.4 11.5 1427
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 pdb entry 2prb 2.4 45.08 3 10187 10125 490 99.98 0.192 0.194 0.192 0.1912 0.235 0.2381 RANDOM 15.601
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.254 r_dihedral_angle_4_deg 14.672 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 6.411 r_scangle_it 2.842 r_scbond_it 1.704 r_angle_refined_deg 1.349 r_mcangle_it 1.202 r_mcbond_it 0.75 r_symmetry_hbond_refined 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.254 r_dihedral_angle_4_deg 14.672 r_dihedral_angle_3_deg 14.086 r_dihedral_angle_1_deg 6.411 r_scangle_it 2.842 r_scbond_it 1.704 r_angle_refined_deg 1.349 r_mcangle_it 1.202 r_mcbond_it 0.75 r_symmetry_hbond_refined 0.385 r_nbtor_refined 0.3 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1356 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 81
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction