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The Structure of Porcine Trypsin in Complex with Crystallization Additives I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Sitting drop vapor diffusion in Cryschem plates. Reservoirs 30% PEG 3350. Drops 3.0 ul of reservoir, plus 2 ul additives oxalic acid, sulfanilic acid, 4-amino benzoic acid mix, plus 3.0 ul of 40 mg/ml stock protein solution of 0.1 M HEPES at pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.2 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59 α = 90 b = 59 β = 90 c = 139.66 γ = 90
Symmetry Space Group P 41 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 295 IMAGE PLATE RIGAKU 2012-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 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 1.28 25.9 91.5 0.054 16.5 5.78 58890 17.39
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 1.28 1.33 0.375 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.28 25.25 1 58253 5905 90.64 0.1165 0.1131 0.1237 0.1466 0.1508 33.48
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 20.5303 f_angle_d 1.1918 f_chiral_restr 0.0989 f_bond_d 0.0097 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1642 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 400
Software Software Software Name Purpose PHENIX refinement d*TREK data reduction Aimless data scaling PHASER phasing