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Crystal structure of human serine/threonine-protein kinase 32A (YANK1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8X 3A8X, 3L9N and 3G51 experimental model PDB 3L9N 3A8X, 3L9N and 3G51 experimental model PDB 3G51 3A8X, 3L9N and 3G51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 20% PEG 3350, 0.2M sodium acetate, 10% ethylene glycol, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.84 56.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.11 α = 90 b = 154.11 β = 90 c = 112.11 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 PIXEL DECTRIS PILATUS 2M Kirkpatrick Baez bimorph mirror pair 2011-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
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 2.29 51.68 95.7 0.089 9.3 3.3 128341 128336 35.7
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 2.29 2.41 97.8 0.638 2 3.2 19231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 3A8X, 3L9N and 3G51 2.29 50.44 2 128336 121915 6421 95.73 0.20636 0.20436 0.2073 0.24449 0.2472 RANDOM 37.803
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] 1.95 0.97 1.95 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.545 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 15.797 r_dihedral_angle_1_deg 6.933 r_angle_refined_deg 1.488 r_angle_other_deg 0.776 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.545 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 15.797 r_dihedral_angle_1_deg 6.933 r_angle_refined_deg 1.488 r_angle_other_deg 0.776 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16848 Nucleic Acid Atoms Solvent Atoms 1003 Heterogen Atoms 242
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling