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D10N variant of beta-phosphoglucomutase from Lactococcus lactis in complex with fructose 1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 290 0.6 mM bPGM-D10N
5 mM MgCl2
50 mM fructose 1,6-bisphosphate
38 % PEG 4000
200 mM sodium acetate
100 mM tris
Crystal Properties Matthews coefficient Solvent content 1.97 37.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.888 α = 90 b = 71.382 β = 90 c = 83.909 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 EIGER2 XE 16M 2020-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 54.429 100 0.151 0.043 0.998 10.5 13.1 20093 18.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.2 1.33 0.379 0.829 1.1 13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 54.429 20040 965 99.915 0.165 0.161 0.1718 0.252 0.2571 28.344
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] -2.477 3.688 -1.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.23 r_dihedral_angle_3_deg 13.539 r_dihedral_angle_1_deg 6.08 r_dihedral_angle_2_deg 4.331 r_angle_refined_deg 1.567 r_angle_other_deg 0.512 r_symmetry_nbd_refined 0.286 r_nbd_other 0.27 r_symmetry_xyhbond_nbd_refined 0.244 r_nbd_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.23 r_dihedral_angle_3_deg 13.539 r_dihedral_angle_1_deg 6.08 r_dihedral_angle_2_deg 4.331 r_angle_refined_deg 1.567 r_angle_other_deg 0.512 r_symmetry_nbd_refined 0.286 r_nbd_other 0.27 r_symmetry_xyhbond_nbd_refined 0.244 r_nbd_refined 0.222 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1708 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing