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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 3.34 63.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.816 α = 90 b = 73.816 β = 90 c = 381.324 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 2006-04-29 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 2.5 20 90.3 0.07 24.3 37974 34291
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) 2.5 2.6 79.2 0.16 12.7
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 PDB ENTRY 2ADV 2.5 19.5 37847 34221 1711 90.42 0.184 0.182 0.181 0.224 0.2208 RANDOM 27.609
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_1_deg 6.275 r_sphericity_free 4.729 r_scangle_it 2.261 r_sphericity_bonded 1.654 r_scbond_it 1.438 r_angle_refined_deg 1.312 r_mcangle_it 1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.48 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_1_deg 6.275 r_sphericity_free 4.729 r_scangle_it 2.261 r_sphericity_bonded 1.654 r_scbond_it 1.438 r_angle_refined_deg 1.312 r_mcangle_it 1.047 r_rigid_bond_restr 0.977 r_mcbond_it 0.614 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5355 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 6
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 HKL-2000 data scaling CNS phasing