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D10N variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by a beryllium triflouride phosphoenzyme analogue to 1.3A resolution.
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 Tris pH 7.5
200mM Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.76 α = 90 b = 53.8 β = 90 c = 81.55 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 2016-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.3 44.3 99 0.056 0.023 0.999 16.1 16.1 57228
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 88.3 1.04 0.542 0.489 1.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WHE 1.3 44.3 54322 2843 98.89 0.13721 0.13564 0.1356 0.16952 0.169 RANDOM 19.59
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] 0.03 -0.18 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.443 r_sphericity_free 32.727 r_dihedral_angle_4_deg 16.109 r_dihedral_angle_3_deg 12.117 r_sphericity_bonded 9.685 r_dihedral_angle_1_deg 5.264 r_long_range_B_refined 3.789 r_long_range_B_other 3.788 r_scangle_other 2.921 r_scbond_other 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.443 r_sphericity_free 32.727 r_dihedral_angle_4_deg 16.109 r_dihedral_angle_3_deg 12.117 r_sphericity_bonded 9.685 r_dihedral_angle_1_deg 5.264 r_long_range_B_refined 3.789 r_long_range_B_other 3.788 r_scangle_other 2.921 r_scbond_other 2.505 r_scbond_it 2.504 r_rigid_bond_restr 2.006 r_mcangle_it 1.95 r_mcangle_other 1.95 r_mcbond_it 1.492 r_mcbond_other 1.49 r_angle_refined_deg 1.482 r_angle_other_deg 0.946 r_chiral_restr 0.175 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1698 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building XDS data reduction xia2 data scaling