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Crystal Structure of Lombricine Kinase, complexed with substrate ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QK1 Homology model built from creatine kinase, 1qk1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 protein at 30 mg/mL in 50mM taurocyamine, 40mM ADP & 5mM MgCl2, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.692 α = 90 b = 77.986 β = 90 c = 141.122 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD double focusing mirrors 2005-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.99997 APS 22-BM
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 2.5 20 99.8 0.122 7.7 5.6 13213 38.2
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 2.5 2.59 98.8 0.174 5.23 4.3 1302
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Homology model built from creatine kinase, 1qk1 2.503 19.994 1.36 13186 482 99.82 0.181 0.178 0.1756 0.25 0.2438 Random 27.429
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] 2.363 -1.193 -1.17
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.4 f_angle_deg 0.69 f_bond_d 0.03
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2866 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing DENZO data reduction