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Crystal structure of an uncharacterized sugar kinase PH1459 from Pyrococcus horikoshii in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EWM PDB ENTRY 3EWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 292 18% PEG 8000, 0.2M Magnesium ACETATE, 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.17 α = 90 b = 54.07 β = 110.95 c = 77.72 γ = 90
Symmetry Space Group C 1 2 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 315r MIRRORS 2009-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 50 99.6 0.075 15 7.3 48828 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.5 0.39 9.3 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3EWM 1.9 29.64 47094 47094 1884 96.2 0.223 0.223 0.2174 0.25 0.255 RANDOM 31.6
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] -3.92 2.22 10.41 -6.49
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.401 c_scbond_it 2.275 c_mcangle_it 2.11 c_mcbond_it 1.366 c_angle_deg 1.3 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.401 c_scbond_it 2.275 c_mcangle_it 2.11 c_mcbond_it 1.366 c_angle_deg 1.3 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4686 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 43
Software Software Software Name Purpose CBASS data collection AMoRE phasing CNS refinement DENZO data reduction HKL-2000 data scaling