☰ Navigation Tabs
T16A variant of beta-phosphoglucomutase from Lactococcus lactis in an open conformer complexed with aluminium tetrafluoride to 1.9 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 Crystallized in:
24-34% PEG 4000,
200 mM sodium acetate,
50 mM TRIS at pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.55 α = 90 b = 52.84 β = 90 c = 78.32 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 2018-02-24 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 1.89 31.46 100 0.096 0.102 0.034 0.999 12.6 8.8 18067
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 1.89 1.92 100 1.698 1.8 0.593 0.58 1.3 9.1
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 1.89 31.46 17149 870 99.83 0.20918 0.20671 0.2137 0.25948 0.2604 RANDOM 40.914
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] 3.52 -2.47 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.138 r_dihedral_angle_4_deg 22.162 r_dihedral_angle_3_deg 14.71 r_long_range_B_other 6.345 r_long_range_B_refined 6.335 r_dihedral_angle_1_deg 5.586 r_scangle_other 5.395 r_scbond_it 3.607 r_scbond_other 3.607 r_mcangle_it 3.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.138 r_dihedral_angle_4_deg 22.162 r_dihedral_angle_3_deg 14.71 r_long_range_B_other 6.345 r_long_range_B_refined 6.335 r_dihedral_angle_1_deg 5.586 r_scangle_other 5.395 r_scbond_it 3.607 r_scbond_other 3.607 r_mcangle_it 3.482 r_mcangle_other 3.481 r_mcbond_it 2.631 r_mcbond_other 2.615 r_angle_refined_deg 1.506 r_angle_other_deg 0.939 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1678 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building MOLREP phasing