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D10N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with tetrafluoroaluminate and beta-G6P to 1.02 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 24-34% PEG 4000
200 mM sodium acetate
50 mM TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.52 α = 90 b = 54.28 β = 90 c = 104.42 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.02 37.52 97.6 0.045 0.054 0.021 0.999 16.1 6.5 106736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.05 82.5 0.917 1.209 0.589 0.542 1.3 3.7
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 2WF6 1.02 35.33 101274 5373 97.6 0.15265 0.15147 0.1597 0.1747 0.1808 RANDOM 16.192
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] 0.51 -0.97 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.317 r_sphericity_bonded 24.744 r_rigid_bond_restr 24.172 r_sphericity_free 19.127 r_dihedral_angle_4_deg 18.779 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 2.631 r_long_range_B_other 2.451 r_scangle_other 2.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.317 r_sphericity_bonded 24.744 r_rigid_bond_restr 24.172 r_sphericity_free 19.127 r_dihedral_angle_4_deg 18.779 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 5.957 r_long_range_B_refined 2.631 r_long_range_B_other 2.451 r_scangle_other 2.392 r_scbond_other 2.138 r_scbond_it 2.137 r_mcangle_other 2.065 r_mcangle_it 1.974 r_mcbond_it 1.912 r_mcbond_other 1.856 r_angle_other_deg 1.52 r_angle_refined_deg 1.507 r_chiral_restr 0.069 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing