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Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XAM pdb entry 2XAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.08M MES, 19.85% PEG3000, 0.17M NaCl, 2.35% benzamidine HCl, Protein: 5mg/mL, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.763 α = 83.01 b = 59.353 β = 89.92 c = 82.232 γ = 63.41
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ VariMax HF 2012-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 50 95.2 0.1 7 3.9 32955 30.89
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 2.54 69.4 0.315 3.4 1166
Refinement Statistics Diffraction ID Structure Solution 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 pdb entry 2XAM 2.6 34.548 0.04 28726 1748 93.4 0.2287 0.2244 0.2162 0.2943 0.2871 RANDOM 32.8169
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] 0.9547 1.2256 -0.3169 -1.128 -6.4045 0.1733
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.18 f_angle_d 1.32 f_chiral_restr 0.074 f_bond_d 0.022 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 130
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing