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Crystal Structure of Serine protease Hepsin in complex with Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Activated hepsin was incubated with 10 mM Benzamidine at 4 oC for 2 hours and concentrated to7 mg/ml using 10 KDa cut off centricon [Millipore]. 1microlit of protein was mixed with 1 microlit of reservoir buffer containing 100 mM sodium Cacodylate (6.0), 22% PEG 3350, and 200 mM ammonium fluoride. Plate clusters with a dimension of 50 micron m x 100 micron m were observed after 2 days of crystallization set up.
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.583 α = 90 b = 47.678 β = 105.3 c = 60.784 γ = 90
Symmetry Space Group P 1 21 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++ 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5
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 2.5 100 87.4 0.074 2.4 2.6 26276 10137
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 2.5 2.59 89.9 0.229 2.2
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 1Z8G 2.5 58.63 9554 485 86.66 0.19165 0.18714 0.1924 0.2815 0.2779 RANDOM 25.094
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] 0.12 -0.09 -0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.373 r_dihedral_angle_4_deg 21.488 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_1_deg 6.887 r_angle_refined_deg 1.695 r_angle_other_deg 0.887 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.373 r_dihedral_angle_4_deg 21.488 r_dihedral_angle_3_deg 16.358 r_dihedral_angle_1_deg 6.887 r_angle_refined_deg 1.695 r_angle_other_deg 0.887 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2625 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing