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Phosphorylated beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 2.4 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 24-34% PEG 4000,
200 mM sodium acetate,
50 mM TRIS pH 7.5,
The crystal was cryoprotected in its original mother liquor plus an additional 25% ethylene glycol and 30mM acetylphosphate.
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.33 α = 90 b = 117.23 β = 97.75 c = 52.93 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 PILATUS3 6M 2015-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97779 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 2.38 58.62 99 0.12 0.165 0.084 0.987 6.7 3.7 18430
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 2.38 2.44 98.9 0.597 0.813 0.438 0.526 3.3
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 2WHE 2.38 58.62 17460 945 99.01 0.22299 0.2188 0.29875 0.2912 RANDOM 40.3
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] 0.47 0.01 -0.24 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.525 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 16.438 r_dihedral_angle_1_deg 6.588 r_long_range_B_other 5.74 r_long_range_B_refined 5.735 r_scangle_other 3.78 r_mcangle_it 3.38 r_mcangle_other 3.379 r_scbond_it 2.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.525 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 16.438 r_dihedral_angle_1_deg 6.588 r_long_range_B_other 5.74 r_long_range_B_refined 5.735 r_scangle_other 3.78 r_mcangle_it 3.38 r_mcangle_other 3.379 r_scbond_it 2.345 r_scbond_other 2.345 r_mcbond_it 2.183 r_mcbond_other 2.182 r_angle_refined_deg 1.539 r_angle_other_deg 0.967 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3368 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building MOLREP phasing