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PKAB3 in complex with pyrrolidine inhibitor 34a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 The droplets, containing 16 mg/ml protein 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide, 0.8 mM PKI peptide and 1mM of the pyrrolidine inhibitor 34a, were equilibrated against 12-26 % (v/v) methanol.
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.852 α = 90 b = 78.431 β = 90 c = 79.506 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 MARMOSAIC 225 mm CCD 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.554 19.608 91.46 0.127 5.94 3.4 51501 20.7097396792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5543 1.5931 0.49 1855
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 1Q61 1.554 19.60775 1.33870116593 51501 1985 91.4581520484 0.209273093362 0.208221335319 0.2105 0.23429993529 0.2346 29.9211444025
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 13.622858442 f_angle_d 1.10137785018 f_chiral_restr 0.0447435485971 f_bond_d 0.00996529345428 f_plane_restr 0.00591263473264
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2863 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing