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T16A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with magnesium trifluoride to 1.6 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 24-34% PEG4000,
200 mM sodium acetate,
50 mM TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.267 α = 90 b = 53.887 β = 90 c = 82.269 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 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.6 45.08 100 0.067 0.072 0.027 0.999 10.8 6.9 28426
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 1.6 1.63 99.4 1.715 1.857 0.703 0.579 6.7
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 2WHE 1.6 45.08 26851 1359 99.31 0.23861 0.23639 0.2449 0.28368 0.2936 RANDOM 33.527
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] 4.17 -2.38 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.337 r_dihedral_angle_4_deg 21.714 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.023 r_long_range_B_other 5.453 r_long_range_B_refined 5.296 r_scangle_other 3.942 r_mcangle_it 2.886 r_mcangle_other 2.885 r_scbond_it 2.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.337 r_dihedral_angle_4_deg 21.714 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.023 r_long_range_B_other 5.453 r_long_range_B_refined 5.296 r_scangle_other 3.942 r_mcangle_it 2.886 r_mcangle_other 2.885 r_scbond_it 2.608 r_scbond_other 2.604 r_mcbond_other 2.043 r_mcbond_it 2.041 r_angle_refined_deg 1.531 r_angle_other_deg 0.954 r_chiral_restr 0.081 r_bond_refined_d 0.012 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 1687 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building MOLREP phasing