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Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y5B PDB ENTRY 1Y5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C.
Crystal Properties Matthews coefficient Solvent content 2.03 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.924 α = 90 b = 56.695 β = 90 c = 66.054 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 CCD Bruker Platinum 135 MIRROR 2006-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 1.5 25.09 99.3 0.05 24.37 7.46 31641 2
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 1.5 1.57 95.9 0.31 3.84 3.32
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Y5B 1.5 25.09 31363 1664 99.8 0.155 0.154 0.1625 0.176 0.186 RANDOM 12.45
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] -0.1 0.08 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.002 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 11.833 r_dihedral_angle_1_deg 6.466 r_scangle_it 4.886 r_scbond_it 3.451 r_mcangle_it 2.691 r_mcbond_it 1.739 r_angle_refined_deg 1.324 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.002 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 11.833 r_dihedral_angle_1_deg 6.466 r_scangle_it 4.886 r_scbond_it 3.451 r_mcangle_it 2.691 r_mcbond_it 1.739 r_angle_refined_deg 1.324 r_angle_other_deg 0.892 r_symmetry_vdw_other 0.247 r_nbd_other 0.193 r_nbd_refined 0.191 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.086 r_nbtor_other 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1708 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 18
Software Software Software Name Purpose BRUKER data reduction SCALEPACK data scaling EPMR phasing SHAKEANDWARP phasing REFMAC refinement