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D170N variant of beta-phosphoglucomutase from Lactococcus lactis complexed with beta-G1P in a closed conformer to 1.2 A.
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 sodium acetate
50mM TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.56 α = 90 b = 55.08 β = 90 c = 105.84 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 2017-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.15 48.86 100 0.126 0.132 0.037 0.999 10.8 12.6 78880
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 1.15 1.17 100 1.986 2.087 0.634 0.562 1.2 10.6
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 1.15 48.86 74925 3872 99.94 0.1516 0.15033 0.1501 0.17623 0.1756 RANDOM 14.394
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] 0.16 -0.5 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.327 r_dihedral_angle_4_deg 22.941 r_sphericity_free 15.9 r_dihedral_angle_3_deg 12.923 r_sphericity_bonded 7.308 r_dihedral_angle_1_deg 5.24 r_long_range_B_refined 2.172 r_scangle_other 2.043 r_long_range_B_other 1.972 r_scbond_it 1.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.327 r_dihedral_angle_4_deg 22.941 r_sphericity_free 15.9 r_dihedral_angle_3_deg 12.923 r_sphericity_bonded 7.308 r_dihedral_angle_1_deg 5.24 r_long_range_B_refined 2.172 r_scangle_other 2.043 r_long_range_B_other 1.972 r_scbond_it 1.744 r_scbond_other 1.743 r_rigid_bond_restr 1.595 r_angle_refined_deg 1.494 r_mcangle_other 1.392 r_mcangle_it 1.378 r_mcbond_it 1.101 r_mcbond_other 1.06 r_angle_other_deg 1.001 r_chiral_restr 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 1689 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing