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Crystal structure of type I phosphatidylinositol 4-phosphate 5-kinase alpha from Zebrafish
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG 20,000
Crystal Properties Matthews coefficient Solvent content 3.46 64.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.946 α = 90 b = 88.946 β = 90 c = 157.074 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315r 2012-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 40 99.5 30.1 13.6 8877
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 3.31 33.309 8877 982 99.02 0.21261 0.20664 0.2033 0.26766 0.2614 RANDOM 70.849
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] -0.12 -0.12 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_3_deg 19.592 r_dihedral_angle_4_deg 18.067 r_long_range_B_other 10.768 r_long_range_B_refined 10.76 r_scangle_other 7.9 r_mcangle_it 6.78 r_mcangle_other 6.778 r_dihedral_angle_1_deg 6.761 r_scbond_it 4.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_3_deg 19.592 r_dihedral_angle_4_deg 18.067 r_long_range_B_other 10.768 r_long_range_B_refined 10.76 r_scangle_other 7.9 r_mcangle_it 6.78 r_mcangle_other 6.778 r_dihedral_angle_1_deg 6.761 r_scbond_it 4.982 r_scbond_other 4.979 r_mcbond_other 4.25 r_mcbond_it 4.248 r_angle_refined_deg 1.404 r_angle_other_deg 0.828 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement