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Crystal structure of trypsin at 225 Kelvin with benzamidine (duplicate)
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 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.005 α = 90 b = 57.109 β = 90 c = 66.509 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 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 1.5 24.423 93.19 0.703 5.6 10 31374
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 24.42 0.703
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 1.5 24.423 31373 1566 93.261 0.266 0.2643 0.2727 0.3008 0.3053 15.48
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] 0.655 -0.731 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.212 r_dihedral_angle_6_deg 13.073 r_dihedral_angle_2_deg 12.06 r_dihedral_angle_1_deg 7.059 r_lrange_it 5.451 r_lrange_other 5.245 r_scangle_it 3.415 r_scangle_other 3.414 r_mcangle_it 2.413 r_mcangle_other 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.212 r_dihedral_angle_6_deg 13.073 r_dihedral_angle_2_deg 12.06 r_dihedral_angle_1_deg 7.059 r_lrange_it 5.451 r_lrange_other 5.245 r_scangle_it 3.415 r_scangle_other 3.414 r_mcangle_it 2.413 r_mcangle_other 2.412 r_scbond_it 2.152 r_scbond_other 2.15 r_angle_refined_deg 1.649 r_mcbond_it 1.482 r_mcbond_other 1.481 r_dihedral_angle_other_2_deg 1.395 r_angle_other_deg 0.556 r_xyhbond_nbd_refined 0.36 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.211 r_symmetry_nbd_other 0.2 r_metal_ion_refined 0.198 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.174 r_nbd_other 0.17 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 173 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing