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Phosphopentomutase S154G variant soaked with 2,3-dideoxyribose 5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8W PDB ENTRY 3M8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 17% PEG3350, 50 mM manganese chloride, 50 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.226 α = 90 b = 76.774 β = 108.32 c = 106.486 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 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 2 50 98.9 0.067 22.2 93620 -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 2 2.07 98.4 0.321 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3M8W 2 20 89875 88860 4579 98.87 0.17049 0.16866 0.207 0.204 RANDOM 28.994
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] 1.27 -0.32 -0.69 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 17.02 r_dihedral_angle_3_deg 13.545 r_long_range_B_refined 5.861 r_dihedral_angle_1_deg 5.501 r_angle_refined_deg 1.155 r_mcangle_it 0.534 r_scbond_it 0.478 r_mcbond_it 0.31 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 17.02 r_dihedral_angle_3_deg 13.545 r_long_range_B_refined 5.861 r_dihedral_angle_1_deg 5.501 r_angle_refined_deg 1.155 r_mcangle_it 0.534 r_scbond_it 0.478 r_mcbond_it 0.31 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9182 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing