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beta-phosphoglucomutase from Lactococcus lactis with citrate, tris and acetate bound
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 PEG 4000, sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), trisodium citrate (50 mM), beta-phosphoglucomutase (0.6 mM)
Crystal Properties Matthews coefficient Solvent content 9.86 87.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.13 α = 90 b = 76.64 β = 90 c = 117.26 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 2018-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97179 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 117.3 97.5 0.098 0.033 0.999 13.7 8.6 27995 24.2
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 2.1 2.16 90.1 0.536 0.574 0.198 0.899 3.7 7.6
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 (All) 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 2.1 46.61 27947 1349 97.332 0.233 0.2299 0.2309 0.2897 0.2901 RANDOM 31.766
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] -0.242 2.269 -2.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.019 r_dihedral_angle_3_deg 15.722 r_dihedral_angle_4_deg 14.703 r_dihedral_angle_1_deg 6.628 r_lrange_other 5.49 r_lrange_it 5.488 r_scangle_it 4.09 r_scangle_other 4.089 r_scbond_it 2.83 r_scbond_other 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.019 r_dihedral_angle_3_deg 15.722 r_dihedral_angle_4_deg 14.703 r_dihedral_angle_1_deg 6.628 r_lrange_other 5.49 r_lrange_it 5.488 r_scangle_it 4.09 r_scangle_other 4.089 r_scbond_it 2.83 r_scbond_other 2.83 r_mcangle_it 2.795 r_mcangle_other 2.795 r_mcbond_it 2.148 r_mcbond_other 2.064 r_angle_refined_deg 1.482 r_angle_other_deg 1.302 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.159 r_nbd_other 0.145 r_ncsr_local_group_1 0.079 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 186 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing PDB_EXTRACT data extraction