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C1B domain of Protein kinase C in complex with prostratin and phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 Screen condition:
0.2 M Ammonium acetate
0.1 M Sodium Phosphate
30% Isopropanol
pH 6.8;
Drop condition:
Protein: 2 mM in MES pH 6.5, 150 mM KCl;
Phosphatidylcholine: 20 mM;
Prostratin: 2.5 mM
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.402 α = 90 b = 25.869 β = 97.29 c = 57.964 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 1 x-ray 120 PIXEL Bruker PHOTON II 2020-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.7 44.6 89.1 0.0558 15.48 3.85 5115
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 1.7 1.8 48.4 0.2636 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ptq 1.7 28.75 1.36 5113 243 89.12 0.174 0.1719 0.174 0.2136 0.2168 17.4806
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 f_dihedral_angle_d 44.539 f_angle_d 1.445 f_chiral_restr 0.089 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 417 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement SAINT data reduction SAINT data scaling PDB_EXTRACT data extraction MOLREP phasing