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Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis inhibited with glucose 6-phosphate and tetrafluoroaluminate to 1.1A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 24-34% PEG 4000
200mM Tris pH 7.2
200mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.54 α = 90 b = 54.28 β = 90 c = 104.67 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 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.1 54.28 99.5 0.07 0.029 0.999 12.5 6.8 87229
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 1.1 1.12 91.6 1.147 0.572 0.484 1.2 4.7
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 2WF5 1.1 52.39 82789 4352 99.44 0.14901 0.14791 0.1482 0.17 0.1701 RANDOM 14.709
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] -0.05 -0.43 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.431 r_sphericity_free 25.325 r_dihedral_angle_4_deg 22.537 r_dihedral_angle_3_deg 10.924 r_sphericity_bonded 7.363 r_dihedral_angle_1_deg 5.264 r_long_range_B_refined 2.808 r_long_range_B_other 2.808 r_scangle_other 1.763 r_mcangle_other 1.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.431 r_sphericity_free 25.325 r_dihedral_angle_4_deg 22.537 r_dihedral_angle_3_deg 10.924 r_sphericity_bonded 7.363 r_dihedral_angle_1_deg 5.264 r_long_range_B_refined 2.808 r_long_range_B_other 2.808 r_scangle_other 1.763 r_mcangle_other 1.563 r_mcangle_it 1.553 r_angle_refined_deg 1.474 r_scbond_it 1.443 r_scbond_other 1.437 r_rigid_bond_restr 1.373 r_mcbond_it 1.117 r_mcbond_other 1.083 r_angle_other_deg 0.923 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 1680 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building XDS data reduction xia2 data scaling