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Crystal structure of Putative S41 protease (YP_211611.1) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.274 α = 90 b = 91.435 β = 90 c = 107.126 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97936 SSRL BL9-2
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 29.311 98 0.068 9.72 3.59 28549 -3 25.478
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 2.07 89.6 0.548 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 29.311 28503 1442 99.48 0.159 0.157 0.1663 0.205 0.2097 RANDOM 37.277
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] -0.07 -1.86 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 12.981 r_dihedral_angle_3_deg 12.264 r_scangle_it 6.987 r_scbond_it 5.288 r_dihedral_angle_1_deg 4.864 r_mcangle_it 3.26 r_mcbond_it 2.397 r_angle_refined_deg 1.794 r_angle_other_deg 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 12.981 r_dihedral_angle_3_deg 12.264 r_scangle_it 6.987 r_scbond_it 5.288 r_dihedral_angle_1_deg 4.864 r_mcangle_it 3.26 r_mcbond_it 2.397 r_angle_refined_deg 1.794 r_angle_other_deg 1.08 r_mcbond_other 0.684 r_nbd_refined 0.226 r_symmetry_vdw_other 0.205 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.186 r_nbd_other 0.184 r_chiral_restr 0.092 r_nbtor_other 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3035 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction autoSHARP phasing