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D170N variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer to 1.4 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
200mM sodium acetate
50mM TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.77 α = 90 b = 119.31 β = 94.8 c = 53.17 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 2017-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.4 52.98 95.4 0.091 0.107 0.055 0.997 8.2 3.8 90031
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 1.4 1.42 95.1 1.243 1.431 0.701 0.462 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WHE 1.4 52.98 85527 4461 95.38 0.1743 0.17177 0.1779 0.22352 0.2241 RANDOM 20.439
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] 0.46 0.2 0.01 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.502 r_sphericity_free 17.635 r_dihedral_angle_4_deg 15.78 r_dihedral_angle_3_deg 13.198 r_sphericity_bonded 13.056 r_dihedral_angle_1_deg 5.442 r_scangle_other 3.483 r_long_range_B_refined 3.389 r_long_range_B_other 3.389 r_scbond_it 2.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.502 r_sphericity_free 17.635 r_dihedral_angle_4_deg 15.78 r_dihedral_angle_3_deg 13.198 r_sphericity_bonded 13.056 r_dihedral_angle_1_deg 5.442 r_scangle_other 3.483 r_long_range_B_refined 3.389 r_long_range_B_other 3.389 r_scbond_it 2.954 r_scbond_other 2.953 r_mcangle_it 2.412 r_mcangle_other 2.412 r_rigid_bond_restr 2.32 r_mcbond_it 1.987 r_mcbond_other 1.986 r_angle_refined_deg 1.502 r_angle_other_deg 0.977 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3378 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing