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Phosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut148591
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X3Y
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 Mut148591, 50 mM HEPES, pH 7.5) was added to the drops and allowed to soak for 90 minutes.
Crystal Properties Matthews coefficient Solvent content 1.75 33.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.906 α = 90 b = 60.906 β = 90 c = 92.728 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 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 1.10000 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 1.402 39.06 99.64 0.06467 0.06761 0.01944 0.999 21.23 12 34849 13.42
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 1.402 1.452 96.54 0.4377 0.4607 0.1396 0.946 3.22 10
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 PDB entry 2X3Y 1.402 39.06 1.38 34846 1745 99.65 0.1569 0.1566 0.156 0.1631 0.1626 16.5
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 14.0467 f_angle_d 0.9642 f_chiral_restr 0.0665 f_plane_restr 0.0283 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1395 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction pointless data scaling Aimless data scaling PHASER phasing