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Beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 Crystals initially grown as open beta-phosphoglucomutase crystals, using 24-32% PEG 4000, 200mM sodium acetate, 50 mM TRIS buffer pH 7.5.
Crystals were cryoprotected in their original mother liquor with the addition of 25% ethylene glycol, 5 mM aluminium chloride and 20 mM sodium fluoride.
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.44 α = 90 b = 53.71 β = 90 c = 80.88 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 2015-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.98 40.44 99.8 0.116 0.156 0.075 0.992 9.5 4.3 71414 19779
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 99.9 0.738 0.969 0.459 0.576 4.3
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 2WHE 1.98 40.44 15929 807 99.79 0.20666 0.20457 0.2137 0.24806 0.2525 RANDOM 24.376
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] 1.12 -1.08 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.341 r_dihedral_angle_4_deg 21.855 r_dihedral_angle_3_deg 14.096 r_dihedral_angle_1_deg 5.848 r_long_range_B_refined 4.49 r_long_range_B_other 4.45 r_scangle_other 3.174 r_mcangle_it 2.475 r_mcangle_other 2.474 r_scbond_other 2.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.341 r_dihedral_angle_4_deg 21.855 r_dihedral_angle_3_deg 14.096 r_dihedral_angle_1_deg 5.848 r_long_range_B_refined 4.49 r_long_range_B_other 4.45 r_scangle_other 3.174 r_mcangle_it 2.475 r_mcangle_other 2.474 r_scbond_other 2.045 r_scbond_it 2.044 r_mcbond_it 1.665 r_mcbond_other 1.665 r_angle_refined_deg 1.483 r_angle_other_deg 0.97 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 1689 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing xia2 data reduction