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Crystal structure of a putative zinc-binding metallo-peptidase (BACCAC_01431) from Bacteroides caccae ATCC 43185 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 30.00% polyethylene glycol 3000, 0.01M EDTA sodium salt, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.096 α = 90 b = 116.117 β = 90 c = 135.823 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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 2.09 29.59 98.3 0.187 7.57 37077 -3 28.33
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 2.0946 2.16 84.9 1.07 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 SAD THROUGHOUT 2.09 29.59 37017 1853 98.96 0.2041 0.2025 0.2085 0.2341 0.241 RANDOM 29.1869
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] -0.08 -1.22 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 19.57 r_dihedral_angle_3_deg 13.538 r_dihedral_angle_1_deg 5.444 r_mcangle_it 2.336 r_angle_refined_deg 1.576 r_mcbond_it 1.563 r_mcbond_other 1.563 r_angle_other_deg 0.974 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 19.57 r_dihedral_angle_3_deg 13.538 r_dihedral_angle_1_deg 5.444 r_mcangle_it 2.336 r_angle_refined_deg 1.576 r_mcbond_it 1.563 r_mcbond_other 1.563 r_angle_other_deg 0.974 r_chiral_restr 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4244 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing