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Crystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 MCSG1 F2: 0.2 M Ammonium Acetate 0.1 M Bis-Tris: HCl, pH 6.5 25 % (w/v) PEG 3350 +3mM 3-phosphoglycerate cryo:15% Ethylene glycol PS38071 24.7mg/mL, 0.4+0.4 puck frn7-12
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.94 α = 90 b = 82.09 β = 97.64 c = 72.41 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 CCD RAYONIX MX-300 Beryllium Lenses 2017-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97856 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 41.045 99 0.048 0.052 0.999 22.98 6.142 84305 -3 12.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 95.5 0.151 0.169 0.987 9.05 5.148
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1o98 1.5 41.045 1.4 84298 2000 99.01 0.1355 0.1349 0.137 0.164 0.164
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.812 f_angle_d 1.108 f_chiral_restr 0.076 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3895 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing