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Exploring trypsin S3 pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZDK PDB entry 2ZDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.1M Imidazole buffer, 0.1M ammonium sulfate, 30% PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2 38.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.6 α = 90 b = 54.6 β = 90 c = 108.4 γ = 120
Symmetry Space Group P 31 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 113 IMAGE PLATE RIGAKU RAXIS IV 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.51 50 97.3 0.046 29.1 5.8 29336 29336 22.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 75.3 0.253 3.7 2 1111
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R PDB entry 2ZDK 1.51 10 28843 27140 1417 96.2 0.139 0.1375 0.1331 0.149 0.191 0.1616 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 11 1591 1867.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.065 s_non_zero_chiral_vol 0.058 s_zero_chiral_vol 0.054 s_similar_adp_cmpnt 0.044 s_anti_bump_dis_restr 0.04 s_from_restr_planes 0.0292 s_angle_d 0.029 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 40
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing