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The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRW DAA native structure (2DRW)
Crystallization Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.468 α = 90 b = 123.274 β = 104.05 c = 116.156 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU JUPITER 210 2005-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 100 0.093 0.096 6.1 93589
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 0.359
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 DAA native structure (2DRW) 2.3 47.67 89171 4735 99.99 0.17373 0.17047 0.1704 0.23524 0.2352 RANDOM 25.417
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 34.809 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_1_deg 6.365 r_scangle_it 2.328 r_scbond_it 1.453 r_angle_refined_deg 1.255 r_mcangle_it 0.975 r_mcbond_it 0.518 r_metal_ion_refined 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.809 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_1_deg 6.365 r_scangle_it 2.328 r_scbond_it 1.453 r_angle_refined_deg 1.255 r_mcangle_it 0.975 r_mcbond_it 0.518 r_metal_ion_refined 0.428 r_nbtor_refined 0.301 r_symmetry_metal_ion_refined 0.272 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16410 Nucleic Acid Atoms Solvent Atoms 1407 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement JUPITOR data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing