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P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with glucose 6-phosphate and trifluoromagnesate
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 7.5 290 PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 mM), beta-phosphoglucomutase (0.4 mM)
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.08 α = 90 b = 54.25 β = 90 c = 104.32 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 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 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 1.04 54.25 99.9 0.067 0.073 0.028 0.999 12.4 6.7 101730 7.445
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 1.04 1.06 99.3 1.138 1.295 0.609 0.544 1.1 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WF5 1.04 52.21 96597 5041 99.81 0.1506 0.1497 0.1685 0.1755 RANDOM 12.63
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] -0.01 -0.36 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 24.108 r_sphericity_free 22.635 r_dihedral_angle_3_deg 11.449 r_sphericity_bonded 6.597 r_dihedral_angle_1_deg 5.25 r_rigid_bond_restr 2.057 r_angle_refined_deg 1.473 r_angle_other_deg 0.908 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 24.108 r_sphericity_free 22.635 r_dihedral_angle_3_deg 11.449 r_sphericity_bonded 6.597 r_dihedral_angle_1_deg 5.25 r_rigid_bond_restr 2.057 r_angle_refined_deg 1.473 r_angle_other_deg 0.908 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1678 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 31
Software Software Software Name Purpose XDS data reduction xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction