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Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.906 α = 90 b = 156.79 β = 95.29 c = 170.161 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 collimating mirror, toroid focusing mirror 2009-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 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 2.11 43.033 99.8 0.122 8.25 3.8 167009 -3 25.198
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) 2.11 2.19 99.9 0.597 2.1
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 2.11 43.033 166973 8604 99.83 0.153 0.151 0.1578 0.193 0.1966 THIN SHELLS 25.45
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] 1.72 0.31 -0.33 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.198 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_4_deg 11.312 r_dihedral_angle_1_deg 5.912 r_scangle_it 5.691 r_scbond_it 4.25 r_mcangle_it 2.242 r_mcbond_it 1.631 r_angle_refined_deg 1.416 r_angle_other_deg 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.198 r_dihedral_angle_3_deg 13.078 r_dihedral_angle_4_deg 11.312 r_dihedral_angle_1_deg 5.912 r_scangle_it 5.691 r_scbond_it 4.25 r_mcangle_it 2.242 r_mcbond_it 1.631 r_angle_refined_deg 1.416 r_angle_other_deg 0.955 r_mcbond_other 0.23 r_symmetry_vdw_refined 0.209 r_symmetry_vdw_other 0.202 r_nbd_refined 0.193 r_nbd_other 0.188 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.1 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23844 Nucleic Acid Atoms Solvent Atoms 2223 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing