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Structural insight on mechanism and diverse substrate selection strategy of ribulokinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 30% PEG4K, 0.2M Sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.683 α = 90 b = 88.84 β = 92.75 c = 230.525 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 ADSC QUANTUM 315 mirrors 2009-08-27 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 mirrors 2009-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9791 NSLS X12C 2 SYNCHROTRON NSLS BEAMLINE X25 0.9791 NSLS X25
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 2.31 50 98.1 0.065 13.4 3.6 99100 99100 29.7
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 2.31 2.35 87.8 0.165 4 2.7 4458
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.31 48.31 99100 97059 2940 96.6 0.224 0.224 0.2256 0.274 0.2741 RANDOM 36
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] 2.09 -1.62 4.09 -6.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 2.52 c_scbond_it 1.79 c_mcangle_it 1.67 c_angle_deg 1.5 c_mcbond_it 1.11 c_improper_angle_d 0.88 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16759 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 10
Software Software Software Name Purpose CBASS data collection SHELXD phasing SHARP phasing CNS refinement Coot model building CCP4 refinement HKL-2000 data reduction SCALEPACK data scaling