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Crystal structure of trypsin at 225 Kelvin with benzamidine
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 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.004 α = 90 b = 57.17 β = 90 c = 66.604 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 225 CMOS BRUKER PHOTON 100 2023-11-06 M LAUE
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 1.479 22.934 96.58 0.798 7.38 10 33953
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 22.93 0.798
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 1.479 22.934 33953 1635 96.578 0.206 0.2043 0.214 0.2315 0.2397 14.823
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] -0.005 -0.001 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.496 r_dihedral_angle_2_deg 16.29 r_dihedral_angle_3_deg 12.268 r_dihedral_angle_1_deg 6.83 r_lrange_it 4.763 r_lrange_other 4.49 r_scangle_it 3.435 r_scangle_other 3.435 r_scbond_it 2.317 r_scbond_other 2.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.496 r_dihedral_angle_2_deg 16.29 r_dihedral_angle_3_deg 12.268 r_dihedral_angle_1_deg 6.83 r_lrange_it 4.763 r_lrange_other 4.49 r_scangle_it 3.435 r_scangle_other 3.435 r_scbond_it 2.317 r_scbond_other 2.315 r_mcangle_it 1.976 r_mcangle_other 1.975 r_angle_refined_deg 1.552 r_dihedral_angle_other_2_deg 1.365 r_mcbond_it 1.361 r_mcbond_other 1.361 r_angle_other_deg 0.547 r_symmetry_xyhbond_nbd_refined 0.302 r_nbd_refined 0.198 r_symmetry_nbd_other 0.196 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.171 r_metal_ion_refined 0.122 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 174 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing