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Crystal structure of product-like, processed N-terminal protease Npro
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SEMET-SUBSTITUTED PROTEIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100MM NA ACETATE, PH8.5 50% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.39 α = 90 b = 41.16 β = 115.38 c = 44.3 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 315r 2011-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.5 40 96.5 0.05 15 3.7 21445 -3
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 1.5 1.54 95.3 0.21 5.2 3.7
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 MAD THROUGHOUT SEMET-SUBSTITUTED PROTEIN 1.5 28.71 20308 1085 96.03 0.17303 0.16959 0.1785 0.23883 0.243 RANDOM 17.747
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] 1.7 -0.78 -2.39 0.73
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.642 r_dihedral_angle_2_deg 36.135 r_rigid_bond_restr 22.638 r_dihedral_angle_3_deg 17.372 r_dihedral_angle_4_deg 16.593 r_sphericity_bonded 12.638 r_dihedral_angle_1_deg 7.414 r_angle_other_deg 3.72 r_angle_refined_deg 2.111 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.642 r_dihedral_angle_2_deg 36.135 r_rigid_bond_restr 22.638 r_dihedral_angle_3_deg 17.372 r_dihedral_angle_4_deg 16.593 r_sphericity_bonded 12.638 r_dihedral_angle_1_deg 7.414 r_angle_other_deg 3.72 r_angle_refined_deg 2.111 r_chiral_restr 0.165 r_gen_planes_other 0.022 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1162 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing