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Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KOB PDB ENTRY 1kob
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283 sodium cacodylate, PEG8000, magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.34 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.992 α = 90 b = 109.909 β = 90 c = 50.063 γ = 90
Symmetry Space Group P 21 21 21
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 4 2002-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 0.9000 SPring-8 BL40B2
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 2.4 20 99.2 0.118 17286 17268 1 2 37.9
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) 2.4 2.53 99.9 0.346
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1kob 2.4 19.979 1 17413 15527 1720 89.2 0.2323 0.2323 0.2323 0.2702 RANDOM 36.3
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] 4.17 -3.05 -1.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 3.33 c_mcangle_it 2.55 c_scbond_it 2.17 c_mcbond_it 1.53 c_angle_deg 1.2 c_improper_angle_d 0.7 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2231 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing