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K145A variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by beryllium trifluoride to 1.3 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
100mM TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.32 α = 90 b = 53.63 β = 90 c = 81.5 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 PILATUS 6M-F 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.31 40.75 99.9 0.068 0.081 0.032 0.999 13.1 6.5 55835
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 1.31 1.34 99.9 1.101 1.335 0.517 0.539 1.5 6.5
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 1.31 40.75 52935 2832 99.89 0.13672 0.13525 0.135 0.1627 0.163 RANDOM 16.262
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] 0.61 -0.38 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.914 r_sphericity_free 21.785 r_dihedral_angle_4_deg 20.832 r_dihedral_angle_3_deg 12.318 r_sphericity_bonded 10.66 r_dihedral_angle_1_deg 5.318 r_long_range_B_other 3.191 r_long_range_B_refined 3.188 r_scangle_other 2.894 r_scbond_it 2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.914 r_sphericity_free 21.785 r_dihedral_angle_4_deg 20.832 r_dihedral_angle_3_deg 12.318 r_sphericity_bonded 10.66 r_dihedral_angle_1_deg 5.318 r_long_range_B_other 3.191 r_long_range_B_refined 3.188 r_scangle_other 2.894 r_scbond_it 2.426 r_scbond_other 2.426 r_rigid_bond_restr 1.915 r_mcangle_it 1.716 r_mcangle_other 1.715 r_angle_refined_deg 1.49 r_mcbond_it 1.332 r_mcbond_other 1.332 r_angle_other_deg 1.08 r_chiral_restr 0.217 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 1685 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building xia2 data reduction MOLREP phasing