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Mutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ADV PDB ENTRY 2ADV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1M Na-cacodylate (pH 6.5), 0.2M magnesium chloride, PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.37 63.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.836 α = 90 b = 73.836 β = 90 c = 384.184 γ = 90
Symmetry Space Group P 41 21 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 210 2005-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.00000 PAL/PLS 4A
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 2.2 50 96.3 0.07 32.9 55819 53754
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) 2.2 2.28 90.4 0.414 5
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 PDB ENTRY 2ADV 2.2 48.39 55714 53658 2733 96.31 0.211 0.209 0.2074 0.251 0.249 RANDOM 34.323
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.755 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 13.771 r_sphericity_free 6.266 r_dihedral_angle_1_deg 6.198 r_sphericity_bonded 3.158 r_rigid_bond_restr 3.004 r_scangle_it 2.947 r_scbond_it 2.78 r_angle_refined_deg 1.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.755 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 13.771 r_sphericity_free 6.266 r_dihedral_angle_1_deg 6.198 r_sphericity_bonded 3.158 r_rigid_bond_restr 3.004 r_scangle_it 2.947 r_scbond_it 2.78 r_angle_refined_deg 1.274 r_mcangle_it 1.271 r_mcbond_it 0.774 r_nbtor_refined 0.307 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5326 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CNS phasing