☰ Navigation Tabs
PglD from Campylobacter jejuni, NCTC 11168, with native substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BSW PDB entry 3BSW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 1.3 M ammonium sulfate, 100 mM cacodylate, pH 6.5 in the resevior; protein solution containing 20 mM HEPES, 150 mM NaCl, pH 7.1, protein concentration of 10 mg/mL, UDP-4-amino-sugar at 5 mM; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 8.3 85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.338 α = 90 b = 162.338 β = 90 c = 162.338 γ = 90
Symmetry Space Group P 43 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 210 Toroidal focusing mirror 2007-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.97840 NSLS X6A
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 2.3 30 100 0.11 5.8 30.2 33079 33079 36.8
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) 2.3 2.38 100 0.607 29.43 30.8 3231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BSW 2.3 29.64 33021 32938 1673 99.75 0.178 0.178 0.178 0.1756 0.191 0.1875 RANDOM 28.606
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.52 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_4_deg 8.056 r_dihedral_angle_1_deg 6.246 r_scangle_it 3.268 r_scbond_it 2.146 r_angle_refined_deg 1.383 r_mcangle_it 1.236 r_mcbond_it 0.637 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.52 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_4_deg 8.056 r_dihedral_angle_1_deg 6.246 r_scangle_it 3.268 r_scbond_it 2.146 r_angle_refined_deg 1.383 r_mcangle_it 1.236 r_mcbond_it 0.637 r_nbtor_refined 0.307 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.154 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1445 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection