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Crystal structure of trypsin at 200 Kelvin with benzamidine (triplicate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.157 α = 90 b = 58.568 β = 90 c = 67.056 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 200 CMOS BRUKER PHOTON 100 2023-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.497 23.088 99.33 0.801 13.65 10 34816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 23.07 0.801
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.497 23.088 34816 1714 99.335 0.18 0.1793 0.188 0.1998 0.2111 10.978
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] 0.065 0.077 -0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.856 r_dihedral_angle_2_deg 11.534 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.958 r_lrange_it 5.09 r_lrange_other 4.646 r_scangle_it 3.557 r_scangle_other 3.557 r_scbond_it 2.415 r_scbond_other 2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.856 r_dihedral_angle_2_deg 11.534 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.958 r_lrange_it 5.09 r_lrange_other 4.646 r_scangle_it 3.557 r_scangle_other 3.557 r_scbond_it 2.415 r_scbond_other 2.414 r_angle_refined_deg 1.803 r_mcangle_it 1.771 r_mcangle_other 1.77 r_dihedral_angle_other_2_deg 1.367 r_mcbond_it 1.18 r_mcbond_other 1.176 r_angle_other_deg 0.656 r_xyhbond_nbd_refined 0.327 r_symmetry_nbd_refined 0.323 r_symmetry_xyhbond_nbd_refined 0.301 r_nbd_refined 0.221 r_symmetry_nbd_other 0.204 r_nbd_other 0.182 r_nbtor_refined 0.178 r_xyhbond_nbd_other 0.164 r_metal_ion_refined 0.12 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing