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D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with native beta-glucose 1,6-bisphosphate intermediate
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,P146A
50 mM MgCl2
10 mM bG16BP
28% PEG 4000
100 mM sodium acetate
100 mM tris
Crystal Properties Matthews coefficient Solvent content 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.023 α = 90 b = 79.663 β = 97.614 c = 79.848 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 PIXEL DECTRIS EIGER2 XE 16M 2023-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9801 Diamond I03
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 1.01 39.83 80.3 0.038 0.016 0.999 26 6.3 166355 7.8
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 1.01 1.03 0.494 0.386 0.743 0.8 1.6
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 1.01 39.83 166313 8222 80.296 0.116 0.1152 0.1125 0.1348 0.1328 14.316
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] -0.047 0.046 0.618 -0.564
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 28.835 r_dihedral_angle_6_deg 14.984 r_dihedral_angle_3_deg 12.209 r_dihedral_angle_1_deg 5.525 r_dihedral_angle_2_deg 4.599 r_angle_refined_deg 1.486 r_angle_other_deg 0.519 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.235 r_nbd_other 0.198
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 28.835 r_dihedral_angle_6_deg 14.984 r_dihedral_angle_3_deg 12.209 r_dihedral_angle_1_deg 5.525 r_dihedral_angle_2_deg 4.599 r_angle_refined_deg 1.486 r_angle_other_deg 0.519 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.235 r_nbd_other 0.198 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.106 r_xyhbond_nbd_refined 0.101 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3412 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing