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Phosphopentomutase V158L variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UN3 PDB ENTRY 3UN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.45 293 20% PEG3350, 50 mM manganese chloride, 50 mM ammonium acetate, 100 mM Bis-Tris, pH 5.45, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.718 α = 90 b = 76.796 β = 108.7 c = 107.175 γ = 90
Symmetry Space Group P 1 21 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 300 mm CCD 2013-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
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 1.89 50 91.5 0.059 14.9 102942 -3
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) 1 1.89 1.92 92.7 0.348 3.4
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 PDB ENTRY 3UN3 1.89 38.78 107299 97975 4956 91.31 0.15738 0.15537 0.1665 0.19737 0.2047 RANDOM 25.414
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] 1.52 -0.42 -0.97 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_4_deg 15.838 r_dihedral_angle_3_deg 14.177 r_long_range_B_other 7.072 r_long_range_B_refined 7.07 r_dihedral_angle_1_deg 6.578 r_scangle_other 4.974 r_mcangle_it 3.352 r_mcangle_other 3.352 r_scbond_it 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_4_deg 15.838 r_dihedral_angle_3_deg 14.177 r_long_range_B_other 7.072 r_long_range_B_refined 7.07 r_dihedral_angle_1_deg 6.578 r_scangle_other 4.974 r_mcangle_it 3.352 r_mcangle_other 3.352 r_scbond_it 3.274 r_scbond_other 3.274 r_mcbond_it 2.38 r_mcbond_other 2.372 r_angle_refined_deg 1.931 r_angle_other_deg 0.895 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9175 Nucleic Acid Atoms Solvent Atoms 746 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing