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Crystal structure of a putative zinc peptidase (NP_812461.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.31 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 277 NANODROP, 0.2M NH4I, 20.0% PEG 3350, No Buffer pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.34 α = 90 b = 67.25 β = 94.28 c = 107.89 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97910 SSRL BL11-1
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 2.28 28.513 93.7 0.043 12.23 31807 -3 39.305
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 2.28 2.36 42.6 0.24 3
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 2.31 28.513 31794 1613 98.43 0.197 0.194 0.1964 0.253 0.2577 RANDOM 29.051
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] -1.27 0.79 0.31 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.636 r_dihedral_angle_4_deg 15.622 r_dihedral_angle_3_deg 13.105 r_dihedral_angle_1_deg 3.898 r_angle_refined_deg 1.732 r_scangle_it 1.511 r_mcangle_it 1.448 r_angle_other_deg 1.03 r_scbond_it 1.03 r_mcbond_it 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.636 r_dihedral_angle_4_deg 15.622 r_dihedral_angle_3_deg 13.105 r_dihedral_angle_1_deg 3.898 r_angle_refined_deg 1.732 r_scangle_it 1.511 r_mcangle_it 1.448 r_angle_other_deg 1.03 r_scbond_it 1.03 r_mcbond_it 0.96 r_symmetry_vdw_refined 0.3 r_symmetry_vdw_other 0.258 r_mcbond_other 0.229 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.198 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.168 r_chiral_restr 0.107 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5230 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction