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D10N variant of beta-phosphoglucomutase from Lactococcus lactis trapped with native beta-glucose 1,6-bisphosphate intermediate to 1.9A 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 7.5
200mM sodium acetate
harvested after ca. 12 weeks
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.71 α = 90 b = 74.49 β = 90 c = 78.56 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 2017-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97948 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 1.86 39.28 100 0.062 0.018 1 25.8 12.9 18807
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 1.86 1.89 99.9 1.972 0.558 0.599 1.2 13.3
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 1.86 39.28 17834 925 99.93 0.20011 0.19781 0.2082 0.24559 0.2463 RANDOM 42.719
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] 2.6 -1.31 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.886 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_4_deg 10.281 r_dihedral_angle_1_deg 6.015 r_long_range_B_refined 5.859 r_long_range_B_other 5.859 r_scangle_other 4.22 r_mcangle_it 3.657 r_mcangle_other 3.657 r_scbond_it 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.886 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_4_deg 10.281 r_dihedral_angle_1_deg 6.015 r_long_range_B_refined 5.859 r_long_range_B_other 5.859 r_scangle_other 4.22 r_mcangle_it 3.657 r_mcangle_other 3.657 r_scbond_it 2.72 r_scbond_other 2.717 r_mcbond_it 2.527 r_mcbond_other 2.525 r_angle_refined_deg 1.494 r_angle_other_deg 0.948 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building XDS data reduction xia2 data scaling