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1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA COMPLEX WITH SAMARIUM (III) CHLORIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QAS APO TRICLINIC PHOSPHOLIPASE C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 clusters formed by mixing - used as seeds in hanging drops 6.5 NEEDLE CLUSTERS WERE FORMED BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (22 MG/ML) WITH A WELL SOLUTION CONSISTING OF 0.1 M NA MES (PH 6.0), 0.2 M LICL, 20% GLYCEROL, AND 12-14 % PEG 8000. FRAGMENTS OF THE NEEDLE CLUSTERS WERE USED TO SEED HANGING DROPS. THE WELL SOLUTION USED FOR THE SEEDING EXPERIMENTS WAS ADJUSTED TO 0.1M NA MES (PH 6.5), 0.2 M LICL, 20 % GLYCEROL, AND 6-8 % PEG 8000., clusters formed by mixing - used as seeds in hanging drops
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.6 α = 66.4 b = 75.1 β = 85.6 c = 86.4 γ = 89.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IIC MIRRORS M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3 60 84.9 0.121 0.121 7.2 2.5 24235 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 73.8 0.248 0.248 2.3 1.8
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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER FREE R APO TRICLINIC PHOSPHOLIPASE C 3 6 22504 1217 0.194 0.194 0.261
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.6 x_angle_deg 1.5 x_improper_angle_d 1.3 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.6 x_angle_deg 1.5 x_improper_angle_d 1.3 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8028 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 5
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing