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guanidinobenzoyl-trypsin acyl-enzyme at 1.13 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GBT PDB entry 1GBT with ligand and solvent removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 ammonium sulfate, bis-tris propane, calcium chloride, 4-nitrophenyl 4-guanidinobenzoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.446 α = 90 b = 57.908 β = 90 c = 66.771 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 100 CCD ADSC QUANTUM 4 2005-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.00000 ALS 8.3.1
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 1.13 43.85 99.97 0.056 0.056 11.9 3.5 75171 75171 -3
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) 1.13 1.19 71.1 0.533 0.533 1.5 1.6
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 THROUGHOUT PDB entry 1GBT with ligand and solvent removed 1.13 43.85 75169 75169 3830 99.97 0.12 0.12 0.119 0.1198 0.146 0.146 RANDOM 8.644
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] 0.81 -0.39 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.355 r_dihedral_angle_4_deg 18.001 r_sphericity_free 13.627 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 6.609 r_scangle_it 5.931 r_rigid_bond_restr 5.558 r_sphericity_bonded 5.3 r_scbond_it 4.63 r_mcangle_it 3.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.355 r_dihedral_angle_4_deg 18.001 r_sphericity_free 13.627 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 6.609 r_scangle_it 5.931 r_rigid_bond_restr 5.558 r_sphericity_bonded 5.3 r_scbond_it 4.63 r_mcangle_it 3.563 r_mcbond_it 2.719 r_angle_other_deg 2.686 r_angle_refined_deg 1.794 r_mcbond_other 1.429 r_nbd_refined 0.364 r_symmetry_vdw_other 0.282 r_symmetry_vdw_refined 0.279 r_symmetry_hbond_refined 0.271 r_nbd_other 0.26 r_xyhbond_nbd_refined 0.211 r_chiral_restr 0.148 r_metal_ion_refined 0.128 r_nbtor_other 0.093 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1674 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 33
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling TRUNCATE data reduction EPMR phasing REFMAC refinement CCP4 data scaling TRUNCATE data scaling