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Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CI7 PDB ENTRY 4CI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.18 M NACL, 90 MM TRIS PH 8.0, 18% PEG 6000, 0.02% W/V 1,4-DIAMINOBUTANE, 0.02% W/V CYSTAMINE DIHYDROCHLORIDE, 0.02% W/V DILOXANIDE FUROATE, 0.02% W/V SARCOSINE, 0.02% W/V SPERMINE, 2MM SODIUM HEPES PH 6.8
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.094 α = 65.22 b = 70.152 β = 89.89 c = 78.852 γ = 80.18
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 2014-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.6 47.3 90.8 0.09 6.8 2.8 110175 1
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 1.6 1.63 49.9 0.47 2.1 2.5
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 PDB ENTRY 4CI7 1.6 71.38 104911 5261 90.8 0.18252 0.18112 0.1895 0.21055 0.2171 RANDOM 15.346
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] -1.33 -0.17 0.15 1.46 -0.53 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_1_deg 6.073 r_mcangle_it 1.552 r_angle_refined_deg 1.274 r_scbond_it 1.062 r_mcbond_it 0.899 r_mcbond_other 0.895 r_angle_other_deg 0.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.291 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_1_deg 6.073 r_mcangle_it 1.552 r_angle_refined_deg 1.274 r_scbond_it 1.062 r_mcbond_it 0.899 r_mcbond_other 0.895 r_angle_other_deg 0.734 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcangle_other 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 6350 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling PHASER phasing