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PglD from Campylobacter jejuni, NCTC 11168, in complex with acetyl coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BSW Citrate-bound model with citrate removed (3BSW)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING 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, acetyl coenzyme A at 5 mM; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.871 α = 90 b = 91.862 β = 90 c = 125.195 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 110 CCD ADSC Toroidal focusing mirror 2007-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.97860 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 1.8 50 100 0.063 9.7 8 60024 60024 18.023
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) 1.8 1.86 99.9 0.361 32 7.5 5897
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 Citrate-bound model with citrate removed (3BSW) 1.8 29.63 60065 59939 3026 99.79 0.186 0.186 0.184 0.1837 0.22 0.2187 RANDOM 19.649
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] 0.06 -0.07 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.872 r_dihedral_angle_3_deg 11.978 r_dihedral_angle_1_deg 6.196 r_dihedral_angle_4_deg 4.522 r_scangle_it 3.218 r_scbond_it 1.989 r_angle_refined_deg 1.62 r_mcangle_it 1.116 r_mcbond_it 0.596 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.872 r_dihedral_angle_3_deg 11.978 r_dihedral_angle_1_deg 6.196 r_dihedral_angle_4_deg 4.522 r_scangle_it 3.218 r_scbond_it 1.989 r_angle_refined_deg 1.62 r_mcangle_it 1.116 r_mcbond_it 0.596 r_nbtor_refined 0.308 r_chiral_restr 0.218 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.127 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4226 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 153
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling