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R49K variant of beta-phosphoglucomutase from Lactococcus lactis complexed aluminium tetrafluoride and beta-G6P to 1.2 A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 24-34% PEG 4000
200mM sodium acetate
50mM TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.21 α = 90 b = 37.22 β = 90 c = 54.22 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 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) 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 1.16 48.1 95.4 0.084 0.09 0.033 0.999 11.2 7.3 70516
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 1.16 1.18 88.5 1.082 1.18 0.46 0.554 6.2
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 2WF6 1.16 48.1 66963 3493 95.35 0.14426 0.14314 0.1431 0.16567 0.1655 RANDOM 16.045
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] 0.32 -0.52 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_sphericity_free 21.317 r_dihedral_angle_4_deg 20.133 r_sphericity_bonded 12.501 r_dihedral_angle_3_deg 10.836 r_dihedral_angle_1_deg 5.615 r_long_range_B_other 3.159 r_long_range_B_refined 3.158 r_scangle_other 2.617 r_scbond_it 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_sphericity_free 21.317 r_dihedral_angle_4_deg 20.133 r_sphericity_bonded 12.501 r_dihedral_angle_3_deg 10.836 r_dihedral_angle_1_deg 5.615 r_long_range_B_other 3.159 r_long_range_B_refined 3.158 r_scangle_other 2.617 r_scbond_it 2.18 r_scbond_other 2.18 r_mcangle_other 2.153 r_mcangle_it 2.142 r_rigid_bond_restr 1.808 r_mcbond_it 1.606 r_mcbond_other 1.566 r_angle_refined_deg 1.502 r_angle_other_deg 1.087 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing