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2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RKD PDB ENTRY 1RKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.7 291 MICROBATCH METHOD AT 291 K. 22.8 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 44% MPD, 10% DIOXANE AND 0.1 M HEPES BUFFER PH 7.7.
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.825 α = 90 b = 84.825 β = 90 c = 168.494 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 SPring-8 BL44B2
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 2.25 50 99.5 0.061 29.6 9.1 32439 -1 39
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 2.25 2.33 97.1 0.4 2.9
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RKD 2.3 44.62 30051 1422 98.8 0.1529 0.1529 0.1575 0.1984 RANDOM 52.8
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] -4.377 -5.06 -4.377 8.753
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 10.64 c_scbond_it 7.53 c_mcangle_it 6.84 c_mcbond_it 4.69 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 10.64 c_scbond_it 7.53 c_mcangle_it 6.84 c_mcbond_it 4.69 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.007 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 109 Heterogen Atoms 6
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing