☰ Navigation Tabs
Substrate-free P146A variant of beta-phosphoglucomutase from Lactococcus lactis
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 7.5 290 PEG 4000 (24% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.5 mM).
Seeded with 10,000x dilution of much smaller protein crystals grown under the same conditions but with 0.2 mM beta-phosphoglucomutase.
Crystal Properties Matthews coefficient Solvent content 9.62 87.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.3 α = 90 b = 56.24 β = 90 c = 77.66 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 2.02 43.95 98.8 0.075 0.081 0.031 0.999 14.4 6.6 15683 32.196
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 2.02 2.05 88.9 0.953 1.09 0.506 0.556 1.2 3.7
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 2.02 43.95 14863 777 98.49 0.2174 0.2156 0.2267 0.2507 0.2623 RANDOM 42.707
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] -0.27 -0.36 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.886 r_dihedral_angle_4_deg 22.923 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_1_deg 6.164 r_angle_refined_deg 1.489 r_angle_other_deg 0.958 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.886 r_dihedral_angle_4_deg 22.923 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_1_deg 6.164 r_angle_refined_deg 1.489 r_angle_other_deg 0.958 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction