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1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 8.6 mg/ml, 0.01M Tris-HCL (pH 8.3), 5mM Thymidine;
Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris (pH 6.5), 25% (w/v) PEG 3350;
Crystal Properties Matthews coefficient Solvent content 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.282 α = 90 b = 107.282 β = 90 c = 63.357 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 100 CCD MARMOSAIC 325 mm CCD 2015-10-19 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) 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 1.45 30 100 0.054 0.054 42.6 12.6 65853 -3 17.4
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 1.45 1.48 100 0.545 5.3 12.1
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 PDB3JYF 1.45 29.91 62495 3280 99.92 0.13301 0.13195 0.1336 0.15302 0.153 RANDOM 21.268
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] -1.07 -1.07 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.575 r_dihedral_angle_4_deg 21.022 r_dihedral_angle_3_deg 10.691 r_sphericity_bonded 9.502 r_long_range_B_refined 7.111 r_long_range_B_other 6.229 r_dihedral_angle_1_deg 5.205 r_rigid_bond_restr 4.585 r_scangle_other 2.449 r_scbond_it 1.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.575 r_dihedral_angle_4_deg 21.022 r_dihedral_angle_3_deg 10.691 r_sphericity_bonded 9.502 r_long_range_B_refined 7.111 r_long_range_B_other 6.229 r_dihedral_angle_1_deg 5.205 r_rigid_bond_restr 4.585 r_scangle_other 2.449 r_scbond_it 1.562 r_scbond_other 1.556 r_angle_refined_deg 1.477 r_mcangle_other 1.477 r_mcangle_it 1.475 r_mcbond_it 0.946 r_mcbond_other 0.939 r_angle_other_deg 0.913 r_chiral_restr 0.105 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.01 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2592 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing BLU-MAX data collection