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Substrate-free D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis
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 7.5 290 0.6 mM bPGM-D10N,P146A
5 mM MgCl2
3 mM AlCl3
20 mM NaF
15 mM glucose 6-phosphate
32 % PEG 4000
200 mM sodium acetate
200 mM tris
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.65 α = 90 b = 117.251 β = 98.637 c = 53.25 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2021-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.679 117.25 98.3 0.089 0.04 0.994 13.8 6.5 52374 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 86.9 0.277 0.6 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.679 52.702 52336 2655 98.202 0.214 0.2108 0.2201 0.2702 0.2789 39.612
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] 2.135 0.763 -1.294 -1.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.93 r_dihedral_angle_3_deg 14.471 r_dihedral_angle_2_deg 8.781 r_dihedral_angle_1_deg 6.149 r_angle_refined_deg 1.671 r_angle_other_deg 0.548 r_nbd_refined 0.232 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.93 r_dihedral_angle_3_deg 14.471 r_dihedral_angle_2_deg 8.781 r_dihedral_angle_1_deg 6.149 r_angle_refined_deg 1.671 r_angle_other_deg 0.548 r_nbd_refined 0.232 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.151 r_symmetry_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.095 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3374 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing