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Phosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut145320
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1 uL protein solution (10 mg/mL GmhA, 500 mM sodium chloride, 10 mM HEPES, pH 7.0) + crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) suspended over 1.5 M ammonium sulfate. Once crystals were grown, 0.2 uL ligand solution (50 mM Mut145320, 50 mM HEPES, pH 7.5) was added to the drops and allowed to soak for 90 minutes.
Crystal Properties Matthews coefficient Solvent content 2.2 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.983 α = 90 b = 84.72 β = 90 c = 127.105 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 2013-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.79 72.981 97.1 0.064 0.07 0.03 0.999 21.75 6.7 73099
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 1.79 1.9 0.57 0.618 0.912
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.79 63.55 1.36 73026 3619 97.78 0.1783 0.177 0.1771 0.2028 0.2032
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 14.67 f_angle_d 1.279 f_chiral_restr 0.076 f_plane_restr 0.013 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5581 Nucleic Acid Atoms Solvent Atoms 1060 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHENIX phasing PDB_EXTRACT data extraction