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Crystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus ATCC 8483 at 1.25 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.05M KH2PO4, 20.00% PEG-8000, No Buffer pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.427 α = 90 b = 47.921 β = 124.62 c = 83.914 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 325 mm CCD 2010-05-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.85503,0.97934,0.97911 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 1.25 31.208 98.6 0.055 12.79 93405 -3 11.53
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 1.25 1.29 89.3 0.522 2.2
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 1.25 31.208 93405 4682 98.9 0.1333 0.1318 0.1399 0.163 0.169 RANDOM 17.0848
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] -0.83 -0.74 1.14 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.851 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 13.301 r_sphericity_free 7.587 r_scangle_it 5.843 r_dihedral_angle_1_deg 5.309 r_sphericity_bonded 5.134 r_scbond_it 4.225 r_mcangle_it 3.173 r_mcbond_it 2.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.851 r_dihedral_angle_4_deg 14.348 r_dihedral_angle_3_deg 13.301 r_sphericity_free 7.587 r_scangle_it 5.843 r_dihedral_angle_1_deg 5.309 r_sphericity_bonded 5.134 r_scbond_it 4.225 r_mcangle_it 3.173 r_mcbond_it 2.342 r_mcbond_other 2.072 r_rigid_bond_restr 1.827 r_angle_refined_deg 1.464 r_angle_other_deg 0.97 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2756 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 19
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing