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Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 25.0000% polyethylene glycol 3350, 0.2070M ammonium iodide, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.057 α = 90 b = 119.221 β = 90 c = 154.314 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 mirror (vertical focusing) 2009-07-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97922,0.97876 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 29.881 99.8 0.099 0.099 9.9 3.7 87284 43.391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.9 0.789 0.789 1 3.8 6398
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 2.3 29.881 87221 4375 99.74 0.203 0.201 0.1999 0.237 0.2346 RANDOM 26.071
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] 2.57 -0.86 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.277 r_dihedral_angle_4_deg 19.274 r_dihedral_angle_3_deg 11.251 r_dihedral_angle_1_deg 4.828 r_scangle_it 1.844 r_scbond_it 1.128 r_angle_refined_deg 1.052 r_mcangle_it 0.806 r_angle_other_deg 0.667 r_mcbond_it 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.277 r_dihedral_angle_4_deg 19.274 r_dihedral_angle_3_deg 11.251 r_dihedral_angle_1_deg 4.828 r_scangle_it 1.844 r_scbond_it 1.128 r_angle_refined_deg 1.052 r_mcangle_it 0.806 r_angle_other_deg 0.667 r_mcbond_it 0.421 r_mcbond_other 0.073 r_chiral_restr 0.061 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12201 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing