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Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.0M ammonium phosphate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.98 58.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.291 α = 90 b = 91.291 β = 90 c = 507.584 γ = 120
Symmetry Space Group P 61 2 2
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 ADSC QUANTUM 4 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
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 25 91 0.065 106991 106991 13.7
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 (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 3GIP 1.8 24.99 106991 106991 5336 91 0.183 0.183 0.1829 0.207 0.2059 RANDOM 17.8
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] 2.88 1.83 2.88 -5.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 2.71 c_scbond_it 1.87 c_mcangle_it 1.43 c_angle_deg 1.4 c_mcbond_it 1 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7110 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection BALBES phasing CNS refinement DENZO data reduction SCALEPACK data scaling