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Beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with magnesium trifluoride to 1.8 A.
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 7.2 291 Initial (open) crystals grown in:
24-32% PEG 4000
200 mM sodium acetate
50 mM TRIS pH 7.5
Crystals cryoprotected in original mother liquor plus:
25% ethylene glycol
15 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.16 α = 90 b = 116.98 β = 98.93 c = 53.11 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 PILATUS 6M-F 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.83 23.4 98.5 0.1 0.108 0.04 0.999 11.6 7 39841
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 1.83 1.86 97.8 1.258 1.355 0.501 0.568 7.2
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 2WHE 1.83 23.31 37867 1943 98.4 0.18477 0.18265 0.1925 0.22583 0.2365 RANDOM 31.521
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 -0.67 0.28 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.223 r_dihedral_angle_4_deg 16.642 r_dihedral_angle_3_deg 12.883 r_long_range_B_refined 5.624 r_long_range_B_other 5.624 r_dihedral_angle_1_deg 5.437 r_scangle_other 4.411 r_mcangle_it 2.814 r_mcangle_other 2.813 r_scbond_it 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.223 r_dihedral_angle_4_deg 16.642 r_dihedral_angle_3_deg 12.883 r_long_range_B_refined 5.624 r_long_range_B_other 5.624 r_dihedral_angle_1_deg 5.437 r_scangle_other 4.411 r_mcangle_it 2.814 r_mcangle_other 2.813 r_scbond_it 2.8 r_scbond_other 2.799 r_mcbond_it 2.007 r_mcbond_other 2 r_angle_refined_deg 1.537 r_angle_other_deg 0.917 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3378 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building MOLREP phasing