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Crystal structure of Inositol Phosphate Multikinase Ipk2 in complex with ADP and Mn2+ from S. cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IEW PDB Entry: 2IEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 100mM HEPES pH7.7, 200mM CaCl2, 28% PEG400
50mM ATP and 50 mM MnCl soaked, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.996 α = 90 b = 184.996 β = 90 c = 49.998 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 CCD ADSC QUANTUM 4 2006-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 30 0.088 11.6 2.8 36366
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 2.398 2.46 0.569 1.6 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB Entry: 2IEW 2.4 30 36366 1922 98.52 0.19534 0.19267 0.1896 0.24593 0.238 RANDOM 47.898
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] 1.52 0.76 1.52 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.946 r_dihedral_angle_4_deg 19.049 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.067 r_scbond_it 1.923 r_angle_refined_deg 1.465 r_mcangle_it 1.461 r_mcbond_it 0.808 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.946 r_dihedral_angle_4_deg 19.049 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_1_deg 6.888 r_scangle_it 3.067 r_scbond_it 1.923 r_angle_refined_deg 1.465 r_mcangle_it 1.461 r_mcbond_it 0.808 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.218 r_nbd_refined 0.21 r_chiral_restr 0.095 r_symmetry_metal_ion_refined 0.028 r_metal_ion_refined 0.027 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4174 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing