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1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein PotD from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1POT pdb entry 1POT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein: 0.3M Sodium chloride, 0.01M HEPES;
Screen: 0.2M Lithium citrate, 2% Tascimate, 20% (w/v) PEG 3350;
Cryo: paratone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.635 α = 75.83 b = 54.347 β = 80.87 c = 76.704 γ = 77.56
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 MARMOSAIC 300 mm CCD Beryllium lenses 2012-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 30 96.8 0.044 33.2 5.9 107591 107591 -3 18.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 95.6 0.554 3.2 4.9 5284
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 (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 1POT 1.5 29.1 102120 102120 5324 96.75 0.15651 0.15651 0.15498 0.1623 0.18554 0.1926 RANDOM 17.102
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] 0.19 -0.37 0.19 0.23 0.43 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.043 r_dihedral_angle_4_deg 15.416 r_dihedral_angle_3_deg 10.585 r_scangle_it 4.656 r_dihedral_angle_1_deg 3.916 r_scbond_it 3.052 r_mcangle_it 1.9 r_angle_refined_deg 1.471 r_mcbond_it 1.152 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.043 r_dihedral_angle_4_deg 15.416 r_dihedral_angle_3_deg 10.585 r_scangle_it 4.656 r_dihedral_angle_1_deg 3.916 r_scbond_it 3.052 r_mcangle_it 1.9 r_angle_refined_deg 1.471 r_mcbond_it 1.152 r_angle_other_deg 0.915 r_mcbond_other 0.389 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5272 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 47
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling