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Crystal structure of Trypsin complexed with benzamide (F01 and F05, cocktail experiment)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0R PDB ENTRY 1S0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.315 α = 90 b = 58.234 β = 90 c = 66.782 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.68 50 99.6 0.036 0.036 7.2 24830 24731 -3 14.8
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 (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 1S0R 1.68 19.86 23431 23382 1238 99.79 0.15893 0.15774 0.1652 0.18218 0.1551 RANDOM 10.043
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] 0.13 -0.28 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.57 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 10.157 r_dihedral_angle_1_deg 6.129 r_scangle_it 1.701 r_scbond_it 1.126 r_angle_refined_deg 1.077 r_angle_other_deg 0.779 r_mcangle_it 0.719 r_mcbond_it 0.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.57 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 10.157 r_dihedral_angle_1_deg 6.129 r_scangle_it 1.701 r_scbond_it 1.126 r_angle_refined_deg 1.077 r_angle_other_deg 0.779 r_mcangle_it 0.719 r_mcbond_it 0.448 r_symmetry_vdw_other 0.244 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.219 r_nbd_other 0.189 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.1 r_nbtor_other 0.084 r_mcbond_other 0.08 r_chiral_restr 0.065 r_xyhbond_nbd_other 0.04 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 30
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling