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D10N,P146A 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,P146A
50 mM MgCl2
50 mM F16BP
32 % PEG 4000
100 mM sodium acetate
100 mM tris
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.12 α = 90 b = 83.757 β = 110.661 c = 38.89 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 2023-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9227 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 1.23 83.76 100 0.074 0.031 0.999 12.3 6.8 55719 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.25 98 0.953 0.315 0.4 5.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.23 41.913 55684 2670 99.898 0.154 0.1516 0.1942 0.187 27.565
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] -0.606 0.505 0.069 0.122
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 20.112 r_dihedral_angle_6_deg 14.827 r_dihedral_angle_3_deg 13.922 r_dihedral_angle_1_deg 5.271 r_dihedral_angle_2_deg 4.84 r_angle_refined_deg 1.185 r_angle_other_deg 0.42 r_nbd_refined 0.228 r_nbd_other 0.226 r_symmetry_nbd_other 0.192
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 20.112 r_dihedral_angle_6_deg 14.827 r_dihedral_angle_3_deg 13.922 r_dihedral_angle_1_deg 5.271 r_dihedral_angle_2_deg 4.84 r_angle_refined_deg 1.185 r_angle_other_deg 0.42 r_nbd_refined 0.228 r_nbd_other 0.226 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.101 r_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_metal_ion_refined 0.028 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing