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Crystal Structure of Spectinomycin Phosphotransferase, APH(9)-Ia, in complex with ADP and Spectinomcyin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I1A apo APH(9)-Ia
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG8000, magnesium acetate, manganese chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.87 57.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.008 α = 90 b = 75.008 β = 90 c = 139.941 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 4r mirrors 2004-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.008 NSLS X8C
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 2.4 50 97 0.066 18.5 6.4 17953 17953 46
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) 2.4 2.49 85.6 0.307 2.9 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 apo APH(9)-Ia 2.4 37.89 18444 17166 1661 93 0.229 0.229 0.2289 0.275 0.2741 RANDOM 54.8
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] 1.76 1.76 -3.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.81 c_mcangle_it 2.7 c_scbond_it 1.89 c_mcbond_it 1.55 c_angle_deg 1.3 c_improper_angle_d 1.08 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.81 c_mcangle_it 2.7 c_scbond_it 1.89 c_mcbond_it 1.55 c_angle_deg 1.3 c_improper_angle_d 1.08 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2614 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 53
Software Software Software Name Purpose CBASS data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling