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Crystal structure of trypsin at 100 Kelvin with benzamidine (quadruplicate)
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, HANGING DROP 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.318 α = 90 b = 58.166 β = 90 c = 66.477 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 298 CMOS BRUKER PHOTON 100 2023-11-01 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 1.498 24.621 99.42 0.874 20.28 10 34364
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 24.61 0.874
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 1.498 24.621 34363 1710 99.375 0.158 0.1567 0.1568 0.1811 0.1816 9.046
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] 0.173 -0.214 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.004 r_dihedral_angle_6_deg 13.267 r_dihedral_angle_3_deg 10.768 r_dihedral_angle_1_deg 7.136 r_lrange_it 5.049 r_lrange_other 4.141 r_scangle_it 2.811 r_scangle_other 2.811 r_scbond_it 1.91 r_scbond_other 1.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.004 r_dihedral_angle_6_deg 13.267 r_dihedral_angle_3_deg 10.768 r_dihedral_angle_1_deg 7.136 r_lrange_it 5.049 r_lrange_other 4.141 r_scangle_it 2.811 r_scangle_other 2.811 r_scbond_it 1.91 r_scbond_other 1.909 r_angle_refined_deg 1.753 r_dihedral_angle_other_2_deg 1.544 r_mcangle_it 1.539 r_mcangle_other 1.539 r_mcbond_it 1.022 r_mcbond_other 1.011 r_angle_other_deg 0.622 r_xyhbond_nbd_refined 0.272 r_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.176 r_nbd_other 0.161 r_symmetry_nbd_refined 0.121 r_metal_ion_refined 0.108 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 334 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing