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Crystal structure of trypsin at 200 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 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.611 α = 90 b = 56.852 β = 90 c = 66.117 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 1.493 24.257 96.5 0.842 8.68 10 32326
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 24.23 0.842
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 1.493 24.257 32326 1617 96.519 0.223 0.2219 0.2222 0.2499 0.25 13.851
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] 0.349 -0.108 -0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.356 r_dihedral_angle_6_deg 13.331 r_dihedral_angle_3_deg 11.392 r_dihedral_angle_1_deg 6.977 r_lrange_it 4.584 r_lrange_other 4.366 r_scangle_it 3.208 r_scangle_other 3.208 r_mcangle_it 2.261 r_mcangle_other 2.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.356 r_dihedral_angle_6_deg 13.331 r_dihedral_angle_3_deg 11.392 r_dihedral_angle_1_deg 6.977 r_lrange_it 4.584 r_lrange_other 4.366 r_scangle_it 3.208 r_scangle_other 3.208 r_mcangle_it 2.261 r_mcangle_other 2.261 r_scbond_it 2.151 r_scbond_other 2.15 r_angle_refined_deg 1.706 r_mcbond_it 1.458 r_mcbond_other 1.458 r_dihedral_angle_other_2_deg 1.235 r_angle_other_deg 0.616 r_xyhbond_nbd_refined 0.352 r_nbd_refined 0.212 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.191 r_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.176 r_metal_ion_refined 0.154 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_gen_planes_refined 0.01 r_bond_refined_d 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 175 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing