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Chicken 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1 (PLCZ1) in complex with calcium and phosphorylated threonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q2VRL0-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M NaHEPES, MOPs acidic pH 7.5, 20% PEG 550 MME & 10% PEG 20,000, 0.2 M Monosaccharides
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.182 α = 90 b = 85.539 β = 112.04 c = 98.433 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 265735 x-ray 100 PIXEL DECTRIS EIGER X 9M 2024-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95307 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.99 50 94.7 0.163 0.178 0.07 0.989 6.4 6 60478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 75.8 0.927 1.031 0.443 0.663 4.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1.99 49.59 57477 2998 94.07 0.17439 0.17287 0.1849 0.20412 0.2141 RANDOM 28.353
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] -0.34 -1.91 -1.77 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.475 r_dihedral_angle_2_deg 8.501 r_long_range_B_refined 7.67 r_long_range_B_other 7.651 r_dihedral_angle_1_deg 7.099 r_scangle_other 6 r_mcangle_it 4.078 r_mcangle_other 4.078 r_scbond_it 3.875 r_scbond_other 3.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.475 r_dihedral_angle_2_deg 8.501 r_long_range_B_refined 7.67 r_long_range_B_other 7.651 r_dihedral_angle_1_deg 7.099 r_scangle_other 6 r_mcangle_it 4.078 r_mcangle_other 4.078 r_scbond_it 3.875 r_scbond_other 3.859 r_mcbond_it 2.748 r_mcbond_other 2.736 r_angle_refined_deg 1.581 r_angle_other_deg 0.507 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4818 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing