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Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Lithium chloride, polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.208 α = 90 b = 41.62 β = 91.58 c = 43.59 γ = 90
Symmetry Space Group C 1 2 1
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-F 2017-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
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 1.9 72.577 99.6 0.099 8.8 3.4 20687
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 1.9 1.94 0.245
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2BDG 2 72.577 16901 897 99.72 0.18747 0.18541 0.1943 0.22584 0.2324 RANDOM 10.645
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 19.053 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 7.107 r_long_range_B_refined 3.908 r_long_range_B_other 3.907 r_scangle_other 2.704 r_angle_refined_deg 1.977 r_mcangle_it 1.731 r_mcangle_other 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 19.053 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 7.107 r_long_range_B_refined 3.908 r_long_range_B_other 3.907 r_scangle_other 2.704 r_angle_refined_deg 1.977 r_mcangle_it 1.731 r_mcangle_other 1.73 r_scbond_it 1.705 r_scbond_other 1.705 r_angle_other_deg 1.092 r_mcbond_it 1.055 r_mcbond_other 1.054 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2078 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction MOLREP phasing