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1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QFK pdb entry 3QFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 295 Protein: 7.0 mg/mL, 0.5M Sodium chloride, Tris-HCl pH 7.2, 0.5 mM TCEP, 1 mM Adenosine; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M Sodium HEPES, 22% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.72 54.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.584 α = 90 b = 86.452 β = 116.86 c = 95.647 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 225 mm CCD beryllium lenses 2014-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.98 30 98 0.102 0.102 16.7 5.1 44896 44896 -3 19
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 1.98 2.01 97.2 0.62 0.62 2.9 5.2 2238
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 pdb entry 3QFK 1.98 29.36 42209 42209 2236 97.96 0.18846 0.1869 0.1977 0.21788 0.2261 RANDOM 31.592
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] 0.29 0.88 5.7 -4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_4_deg 11.416 r_dihedral_angle_3_deg 9.598 r_long_range_B_refined 6.308 r_long_range_B_other 6.143 r_dihedral_angle_1_deg 3.116 r_scangle_other 2.218 r_mcangle_it 1.875 r_mcangle_other 1.875 r_angle_refined_deg 1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_4_deg 11.416 r_dihedral_angle_3_deg 9.598 r_long_range_B_refined 6.308 r_long_range_B_other 6.143 r_dihedral_angle_1_deg 3.116 r_scangle_other 2.218 r_mcangle_it 1.875 r_mcangle_other 1.875 r_angle_refined_deg 1.493 r_scbond_it 1.423 r_scbond_other 1.422 r_mcbond_it 1.154 r_mcbond_other 1.154 r_angle_other_deg 0.746 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4092 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling