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R49K variant of beta-phosphoglucomutase from Lactococcus lactis complexed with magnesium trifluoride and beta-G6P 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 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.55 α = 90 b = 54.3 β = 90 c = 104.2 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 PILATUS3 6M 2016-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97629 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 37.55 98.5 0.068 0.073 0.027 0.999 14.2 7.1 73452
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 92.3 1.345 1.475 0.591 0.515 5.9
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 1.16 35.35 69661 3716 98.35 0.13387 0.13237 0.1325 0.16356 0.163 RANDOM 15.919
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] -0.26 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.519 r_sphericity_free 21.307 r_dihedral_angle_4_deg 16.595 r_dihedral_angle_3_deg 11.698 r_sphericity_bonded 10.956 r_dihedral_angle_1_deg 5.496 r_long_range_B_refined 3.499 r_long_range_B_other 3.498 r_scangle_other 2.527 r_mcangle_other 2.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.519 r_sphericity_free 21.307 r_dihedral_angle_4_deg 16.595 r_dihedral_angle_3_deg 11.698 r_sphericity_bonded 10.956 r_dihedral_angle_1_deg 5.496 r_long_range_B_refined 3.499 r_long_range_B_other 3.498 r_scangle_other 2.527 r_mcangle_other 2.086 r_mcangle_it 2.08 r_scbond_other 1.968 r_scbond_it 1.967 r_rigid_bond_restr 1.71 r_mcbond_it 1.608 r_mcbond_other 1.591 r_angle_refined_deg 1.506 r_angle_other_deg 1.055 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing