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Structure of the KLK1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M (NH4)2SO4, 0.1M Bis-Tris pH6.5, 25% PEG3,350.
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.708 α = 90 b = 68.59 β = 90 c = 80.458 γ = 90
Symmetry Space Group P 2 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 100 PIXEL DECTRIS EIGER X 9M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.180820 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 45.75 88.1 0.167 13.9 11.6 9127
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.981
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 2.401 45.75 9103 439 87.782 0.183 0.1803 0.1872 0.2451 0.2483 32.974
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] -2.543 -1.631 4.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.159 r_dihedral_angle_6_deg 10.641 r_dihedral_angle_1_deg 6.489 r_dihedral_angle_2_deg 4.742 r_lrange_it 4.44 r_lrange_other 4.434 r_scangle_it 2.698 r_scangle_other 2.697 r_mcangle_other 2.295 r_mcangle_it 2.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.159 r_dihedral_angle_6_deg 10.641 r_dihedral_angle_1_deg 6.489 r_dihedral_angle_2_deg 4.742 r_lrange_it 4.44 r_lrange_other 4.434 r_scangle_it 2.698 r_scangle_other 2.697 r_mcangle_other 2.295 r_mcangle_it 2.294 r_scbond_it 1.538 r_scbond_other 1.537 r_mcbond_it 1.315 r_mcbond_other 1.311 r_angle_refined_deg 0.996 r_angle_other_deg 0.353 r_symmetry_nbd_other 0.189 r_nbd_refined 0.174 r_nbtor_refined 0.17 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.092 r_symmetry_nbtor_other 0.089 r_symmetry_nbd_refined 0.088 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1855 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing