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Phosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut148233
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8V2T
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) + 1 uL crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) were mixed and suspended over 1.5 M ammonium sulfate. Once crystals were grown, 0.2 uL ligand solution (50 mM Mut148233, 50 mM HEPES, pH 7.5) was added to the drops and allowed to soak for 90 minutes.
Crystal Properties Matthews coefficient Solvent content 1.74 33.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.972 α = 90 b = 60.972 β = 90 c = 92.429 γ = 90
Symmetry Space Group P 42 21 2
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 ADSC QUANTUM 315 2013-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 36.83 99.68 0.03807 0.03959 0.01072 1 41.13 13.7 42503 10.67
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 1.357 100 0.2714 0.2819 0.07575 0.985 8.89 13.7
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 1.31 36.83 1.34 42502 2147 99.59 0.1615 0.1609 0.1606 0.1725 0.1716 15.14
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 13.8867 f_angle_d 1.097 f_chiral_restr 0.071 f_plane_restr 0.0305 f_bond_d 0.0099
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1404 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction pointless data scaling Aimless data scaling PHASER phasing