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Crystal structure of KLK6 in complex with compound 16a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.20 M trimethylamine N-oxide, 0.1 M Tris-HCl pH8.5, 20% PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 1.91 35.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.37 α = 81.9 b = 39.97 β = 84.95 c = 65.07 γ = 70.71
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 PILATUS 2M 2021-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.965 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.47 64.36 94.7 0.082 0.097 0.995 9.2 3.407 57658 16.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.51 79.7 1.214 1.451 0.36 1.3 3.173
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VFE 1.47 64.36 1.91 57643 2881 94.68 0.1735 0.1719 0.1719 0.2042 0.2043 20.8
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.7667 f_angle_d 1.237 f_chiral_restr 0.102 f_plane_restr 0.0083 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3365 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction