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Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 protein (10 mg/ml) in 10mM NaHepes, pH 7.5, 1mM EDTA, 1mM DTT; crystallization in 22% polyethylene glycol 4000, 0.1 M Tris-HCl, 0.2 M Lithium sulfate. Glycerol added as cryoprotectant., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.77 α = 90 b = 132.3 β = 90 c = 140.97 γ = 90
Symmetry Space Group I 2 2 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 BRANDEIS 2000-08-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9790, 0.9787, 0.9500 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 50 97.8 0.089 10 5.4 28788 28788 33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 95.9 0.171 4.2 3494
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 20 2 27928 26906 1581 0.176 0.1957 0.258 0.2703 random 34
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 c_angle_deg 1.6 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5448 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX model building MLPHARE phasing DM model building CNS refinement SHELX phasing DM phasing