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Crystal structure of membrane-type serine protease 1 (MT-SP1) in complex with the Fab Inhibitor S4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BN9 PDB ENTRIES: 3BN9, 2JB5, 3KDM experimental model PDB 2JB5 PDB ENTRIES: 3BN9, 2JB5, 3KDM experimental model PDB 3KDM PDB ENTRIES: 3BN9, 2JB5, 3KDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 50 mM Tris, 100 mM NaCl, 5% glycerol, no buffer was added for crystallization, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.161 α = 90 b = 83.988 β = 91.45 c = 101.394 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 CCD ADSC QUANTUM 210 MIRRORS 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.4 43.393 84.5 0.058 16 3.7 88531 1 19.6
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 1.4 1.46 80 0.176 8 3.1
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 (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 PDB ENTRIES: 3BN9, 2JB5, 3KDM 1.5 28.64 87943 88531 4447 84.5 0.19 0.188 0.1875 0.228 0.2259 RANDOM 23.94
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 37.266 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_4_deg 13.004 r_dihedral_angle_1_deg 6.638 r_scangle_it 3.758 r_scbond_it 2.452 r_mcangle_it 1.632 r_angle_refined_deg 1.606 r_mcbond_it 0.952 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.266 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_4_deg 13.004 r_dihedral_angle_1_deg 6.638 r_scangle_it 3.758 r_scbond_it 2.452 r_mcangle_it 1.632 r_angle_refined_deg 1.606 r_mcbond_it 0.952 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5157 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction