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Crystal structure of the S/T protein kinase PknG from Corynebacterium glutamicum in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y0X 4Y0X, 2PZI experimental model PDB 2PZI 4Y0X, 2PZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 100 mM Tris-HCl, 17% w/v PEG 20 k, 100 mM MgCl2, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.663 α = 90 b = 42.741 β = 95.311 c = 175.327 γ = 90
Symmetry Space Group P 1 21 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 2013-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 46.68 99.1 0.086 0.102 0.054 0.996 9.9 3.4 78954 30.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 0.514 0.64 0.374 0.675 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Y0X, 2PZI 2.2 43.02 1.34 78937 4029 98.97 0.2111 0.2093 0.2097 0.2457 0.2469 37.76
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4224 f_angle_d 0.5624 f_chiral_restr 0.0414 f_plane_restr 0.0042 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10369 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing