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Crystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S1U 6S1U, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 Protein solution: 5.0 mg/mL protein with 1.4-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 5 mM TCEP, 10 mM Tris buffer pH 7.4;
Reservoir solution: 0.1 M sodium citrate buffer, 25% propan-2-ol, 5 mM TCEP;
Crystal Properties Matthews coefficient Solvent content 2.378 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.947 α = 90 b = 29.504 β = 101.71 c = 85.39 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 PIXEL DECTRIS PILATUS 6M 2013-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.64 48.91 99.3 0.043 0.05 0.999 14.36 3.65 30408
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 1.64 1.74 98.3 0.826 0.97 0.568 1.37 3.56
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 6S1U, chain A 1.64 48.91 29403 1004 99.29 0.18006 0.1787 0.1895 0.22018 0.2275 RANDOM 40.063
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] 1.35 -0.82 -0.76 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_3_deg 15.046 r_long_range_B_refined 8.846 r_long_range_B_other 8.831 r_dihedral_angle_1_deg 8.619 r_dihedral_angle_4_deg 8.397 r_scangle_other 5.247 r_mcangle_it 4.144 r_mcangle_other 4.142 r_scbond_it 3.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_dihedral_angle_3_deg 15.046 r_long_range_B_refined 8.846 r_long_range_B_other 8.831 r_dihedral_angle_1_deg 8.619 r_dihedral_angle_4_deg 8.397 r_scangle_other 5.247 r_mcangle_it 4.144 r_mcangle_other 4.142 r_scbond_it 3.463 r_scbond_other 3.454 r_mcbond_it 2.754 r_mcbond_other 2.749 r_angle_refined_deg 1.701 r_angle_other_deg 1.36 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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 1733 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing