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Crystal structure of Textilinin-1, a Kunitz-type serine protease inhibitor from the Australian Common Brown snake venom, in complex with trypsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M HEPES-Na, 1.4M tri-sodium citrate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.32 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.838 α = 90 b = 79.838 β = 90 c = 107.394 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE RIGAKU RAXIS IV Confocal X-ray optics Osmic mirrors 2006-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.63 50 97.1 0.055 0.055 22.2 3.85 49994 49994
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.63 1.69 90.7 0.494 0.494 11.47 4534
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3PTN 1.64 37.42 45055 45055 2413 96.46 0.21608 0.21438 0.21274 0.2109 0.24548 0.2449 RANDOM 26.218
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 r_dihedral_angle_2_deg 38.092 r_dihedral_angle_4_deg 19.027 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 6.581 r_scangle_it 4.05 r_scbond_it 2.809 r_mcangle_it 1.839 r_angle_refined_deg 1.669 r_mcbond_it 1.133 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.092 r_dihedral_angle_4_deg 19.027 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 6.581 r_scangle_it 4.05 r_scbond_it 2.809 r_mcangle_it 1.839 r_angle_refined_deg 1.669 r_mcbond_it 1.133 r_nbtor_refined 0.302 r_nbd_refined 0.276 r_symmetry_hbond_refined 0.233 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.135 r_metal_ion_refined 0.067 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2073 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing