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2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 VAPOUR-DIFFUSION SITTING DROP AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM KDG AND 5 MM AMP-PNP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND LIGANDS
Crystal Properties Matthews coefficient Solvent content 2.53 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.321 α = 90 b = 84.321 β = 90 c = 168.701 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU IMAGE PLATE R-AXISV 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 2.1 30 97.9 0.056 19.6 4.58 38730 -0.4 13.1
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 2.1 2.18 96.2 0.355 2.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY V19 2.1 29.82 37822 1852 95.7 0.1798 0.1798 0.2677 RANDOM 51.4
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] -3.709 -3.064 -3.709 7.417
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 11.51 c_scbond_it 8.64 c_mcangle_it 8.46 c_mcbond_it 5.94 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 11.51 c_scbond_it 8.64 c_mcangle_it 8.46 c_mcbond_it 5.94 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.008 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_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4594 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 78
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing